3T9G

The crystal structure of family 3 pectate lyase from Caldicellulosiruptor bescii

PDB DOI: https://doi.org/10.2210/pdb3T9G/pdb

Classification: LYASE
Organism(s): Caldicellulosiruptor bescii
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2011-08-02 Released: 2012-05-09
Deposition Author(s): Alahuhta, P.M., Lunin, V.V.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.50 Å
R-Value Free: 0.178
R-Value Work: 0.143
R-Value Observed: 0.145

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

Literature

A 1.5 A resolution X-ray structure of the catalytic module of Caldicellulosiruptor bescii family 3 pectate lyase.

Alahuhta, M., Chandrayan, P., Kataeva, I., Adams, M.W., Himmel, M.E., Lunin, V.V.

(2011) Acta Crystallogr Sect F Struct Biol Cryst Commun 67: 1498-1500

PubMed: 22139151 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1107/S1744309111038449
Primary Citation of Related Structures:
3T9G

PubMed Abstract:
A 1.5 Å resolution X-ray structure of the catalytic module of Caldicellulosiruptor bescii family 3 pectate lyase is reported (PDB entry 3t9g). The resulting structure was refined to an R factor of 0.143 and an R(free) of 0.178. Structural analysis shows that this new structure is very similar to the previously solved structure of a family 3 pectate lyase from Bacillus sp. strain KSM-P15 (PDB entry 1ee6), with a root-mean-square deviation of 0.93 Å and a sequence identity of 53%. This structural similarity is significant considering that C. bescii is a hyperthermophile and Bacillus sp. is a mesophile.

Organizational Affiliation

BioSciences Center, National Renewable Energy Laboratory, Golden, CO 80401, USA.

Macromolecule Content

Total Structure Weight: 44.22 kDa
Atom Count: 3,980
Modelled Residue Count: 391
Deposited Residue Count: 392
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Pectate lyase	A, B	196	Caldicellulosiruptor bescii	Mutation(s): 0 Gene Names: Athe_1854, Cbes_1854 EC: 4.2.2.2
UniProt
Find proteins for B9MKT4 (Caldicellulosiruptor bescii (strain ATCC BAA-1888 / DSM 6725 / KCTC 15123 / Z-1320)) Explore B9MKT4 Go to UniProtKB: B9MKT4
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	B9MKT4
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 9 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
MRD Query on MRD Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain M [auth B] SDF format, chain D [auth A] SDF format, chain P [auth B] MOL2 format, chain E [auth A] MOL2 format, chain M [auth B] MOL2 format, chain D [auth A] MOL2 format, chain P [auth B] mmCIF format, chain E [auth A] mmCIF format, chain M [auth B] mmCIF format, chain D [auth A] mmCIF format, chain P [auth B]	D [auth A], E [auth A], M [auth B], P [auth B]	(4R)-2-METHYLPENTANE-2,4-DIOL C₆ H₁₄ O₂ SVTBMSDMJJWYQN-RXMQYKEDSA-N		Interactions Focus chain D [auth A] Focus chain E [auth A] Focus chain M [auth B] Focus chain P [auth B] Interactions & Density Focus chain D [auth A] Focus chain E [auth A] Focus chain M [auth B] Focus chain P [auth B]
MPD Query on MPD Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain N [auth B] SDF format, chain O [auth B] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain N [auth B] MOL2 format, chain O [auth B] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain N [auth B] mmCIF format, chain O [auth B]	F [auth A], G [auth A], N [auth B], O [auth B]	(4S)-2-METHYL-2,4-PENTANEDIOL C₆ H₁₄ O₂ SVTBMSDMJJWYQN-YFKPBYRVSA-N		Interactions Focus chain F [auth A] Focus chain G [auth A] Focus chain N [auth B] Focus chain O [auth B] Interactions & Density Focus chain F [auth A] Focus chain G [auth A] Focus chain N [auth B] Focus chain O [auth B]
PO4 Query on PO4 Download Ideal Coordinates CCD File SDF format, chain AA [auth B] SDF format, chain Z [auth B] MOL2 format, chain AA [auth B] MOL2 format, chain Z [auth B] mmCIF format, chain AA [auth B] mmCIF format, chain Z [auth B]	AA [auth B], Z [auth B]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain AA [auth B] Focus chain Z [auth B] Interactions & Density Focus chain AA [auth B] Focus chain Z [auth B]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain J [auth A] SDF format, chain V [auth B] SDF format, chain I [auth A] SDF format, chain W [auth B] MOL2 format, chain J [auth A] MOL2 format, chain V [auth B] MOL2 format, chain I [auth A] MOL2 format, chain W [auth B] mmCIF format, chain J [auth A] mmCIF format, chain V [auth B] mmCIF format, chain I [auth A] mmCIF format, chain W [auth B]	I [auth A], J [auth A], V [auth B], W [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain I [auth A] Focus chain J [auth A] Focus chain V [auth B] Focus chain W [auth B] Interactions & Density Focus chain I [auth A] Focus chain J [auth A] Focus chain V [auth B] Focus chain W [auth B]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain R [auth B] SDF format, chain Q [auth B] MOL2 format, chain R [auth B] MOL2 format, chain Q [auth B] mmCIF format, chain R [auth B] mmCIF format, chain Q [auth B]	Q [auth B], R [auth B]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain Q [auth B] Focus chain R [auth B] Interactions & Density Focus chain Q [auth B] Focus chain R [auth B]
ACT Query on ACT Download Ideal Coordinates CCD File SDF format, chain X [auth B] SDF format, chain Y [auth B] MOL2 format, chain X [auth B] MOL2 format, chain Y [auth B] mmCIF format, chain X [auth B] mmCIF format, chain Y [auth B]	X [auth B], Y [auth B]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain X [auth B] Focus chain Y [auth B] Interactions & Density Focus chain X [auth B] Focus chain Y [auth B]
CA Query on CA Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain K [auth B] MOL2 format, chain C [auth A] MOL2 format, chain K [auth B] mmCIF format, chain C [auth A] mmCIF format, chain K [auth B]	C [auth A], K [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain K [auth B] Interactions & Density Focus chain C [auth A] Focus chain K [auth B]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain L [auth B] MOL2 format, chain L [auth B] mmCIF format, chain L [auth B]	L [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain L [auth B] Interactions & Density Focus chain L [auth B]
NA Query on NA Download Ideal Coordinates CCD File SDF format, chain T [auth B] SDF format, chain U [auth B] SDF format, chain H [auth A] SDF format, chain S [auth B] MOL2 format, chain T [auth B] MOL2 format, chain U [auth B] MOL2 format, chain H [auth A] MOL2 format, chain S [auth B] mmCIF format, chain T [auth B] mmCIF format, chain U [auth B] mmCIF format, chain H [auth A] mmCIF format, chain S [auth B]	H [auth A], S [auth B], T [auth B], U [auth B]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Focus chain S [auth B] Focus chain T [auth B] Focus chain U [auth B] Interactions & Density Focus chain H [auth A] Focus chain S [auth B] Focus chain T [auth B] Focus chain U [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.50 Å
R-Value Free: 0.178
R-Value Work: 0.143
R-Value Observed: 0.145
Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 36.514	α = 90
b = 146.685	β = 90
c = 162.159	γ = 90

Software Package:

Software Name	Purpose
PROTEUM PLUS	data collection
MOLREP	phasing
REFMAC	refinement
SAINT	data reduction
PROTEUM PLUS	data scaling

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2012-05-09

Deposition Author(s):

Alahuhta, P.M.

Lunin, V.V.

Revision History (Full details and data files)

Version 1.0: 2012-05-09
Type: Initial release
Version 1.1: 2023-09-13
Changes: Data collection, Database references, Derived calculations, Refinement description