4DU6 | pdb_00004du6

Crystal structure of GTP cyclohydrolase I from Yersinia pestis complexed with GTP

PDB DOI: https://doi.org/10.2210/pdb4DU6/pdb

Classification: HYDROLASE
Organism(s): Yersinia pestis CO92
Expression System: Escherichia coli BL21
Mutation(s): No

Deposited: 2012-02-21 Released: 2012-03-21
Deposition Author(s): Maltseva, N., Kim, Y., Kwon, K., Anderson, W.F., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.11 Å
R-Value Free:
0.225 (Depositor), 0.220 (DCC)
R-Value Work:
0.180 (Depositor), 0.180 (DCC)
R-Value Observed:
0.182 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

Literature

Crystal structure of GTP cyclohydrolase I from Yersinia pestis complexed with GTP

Maltseva, N., Kim, Y., Kwon, K., Anderson, W.F., Joachimiak, A., CSGID

To be published.

Macromolecule Content

Total Structure Weight: 128.96 kDa
Atom Count: 9,163
Modelled Residue Count: 1,084
Deposited Residue Count: 1,115
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
GTP cyclohydrolase 1	A, B, C, D, E	223	Yersinia pestis CO92	Mutation(s): 0 Gene Names: folE, YPTB1520 EC: 3.5.4.16
UniProt
Find proteins for Q8ZG15 (Yersinia pestis) Explore Q8ZG15 Go to UniProtKB: Q8ZG15
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q8ZG15
Sequence Annotations Expand
Reference Sequence LOADING

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GTP Query on GTP Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain K [auth B] SDF format, chain N [auth C] SDF format, chain T [auth D] SDF format, chain X [auth E] MOL2 format, chain F [auth A] MOL2 format, chain K [auth B] MOL2 format, chain N [auth C] MOL2 format, chain T [auth D] MOL2 format, chain X [auth E] mmCIF format, chain F [auth A] mmCIF format, chain K [auth B] mmCIF format, chain N [auth C] mmCIF format, chain T [auth D] mmCIF format, chain X [auth E]	F [auth A], K [auth B], N [auth C], T [auth D], X [auth E]	GUANOSINE-5'-TRIPHOSPHATE C₁₀ H₁₆ N₅ O₁₄ P₃ XKMLYUALXHKNFT-UUOKFMHZSA-N		Interactions Focus chain F [auth A] Focus chain K [auth B] Focus chain N [auth C] Focus chain T [auth D] Focus chain X [auth E] Interactions & Density Focus chain F [auth A] Focus chain K [auth B] Focus chain N [auth C] Focus chain T [auth D] Focus chain X [auth E]
TRS Query on TRS Download Ideal Coordinates CCD File SDF format, chain J [auth B] SDF format, chain O [auth C] SDF format, chain U [auth D] MOL2 format, chain J [auth B] MOL2 format, chain O [auth C] MOL2 format, chain U [auth D] mmCIF format, chain J [auth B] mmCIF format, chain O [auth C] mmCIF format, chain U [auth D]	J [auth B], O [auth C], U [auth D]	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C₄ H₁₂ N O₃ LENZDBCJOHFCAS-UHFFFAOYSA-O		Interactions Focus chain J [auth B] Focus chain O [auth C] Focus chain U [auth D] Interactions & Density Focus chain J [auth B] Focus chain O [auth C] Focus chain U [auth D]
PEG Query on PEG Download Ideal Coordinates CCD File SDF format, chain I [auth B] MOL2 format, chain I [auth B] mmCIF format, chain I [auth B]	I [auth B]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain I [auth B] Interactions & Density Focus chain I [auth B]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain H [auth B] SDF format, chain M [auth C] SDF format, chain Q [auth C] SDF format, chain R [auth C] SDF format, chain S [auth D] SDF format, chain W [auth E] MOL2 format, chain G [auth A] MOL2 format, chain H [auth B] MOL2 format, chain M [auth C] MOL2 format, chain Q [auth C] MOL2 format, chain R [auth C] MOL2 format, chain S [auth D] MOL2 format, chain W [auth E] mmCIF format, chain G [auth A] mmCIF format, chain H [auth B] mmCIF format, chain M [auth C] mmCIF format, chain Q [auth C] mmCIF format, chain R [auth C] mmCIF format, chain S [auth D] mmCIF format, chain W [auth E]	G [auth A] H [auth B] M [auth C] Q [auth C] R [auth C] G [auth A], H [auth B], M [auth C], Q [auth C], R [auth C], S [auth D], W [auth E]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain H [auth B] Focus chain M [auth C] Focus chain Q [auth C] Focus chain R [auth C] Focus chain S [auth D] Focus chain W [auth E] Interactions & Density Focus chain G [auth A] Focus chain H [auth B] Focus chain M [auth C] Focus chain Q [auth C] Focus chain R [auth C] Focus chain S [auth D] Focus chain W [auth E]
CA Query on CA Download Ideal Coordinates CCD File SDF format, chain L [auth B] SDF format, chain P [auth C] SDF format, chain V [auth D] MOL2 format, chain L [auth B] MOL2 format, chain P [auth C] MOL2 format, chain V [auth D] mmCIF format, chain L [auth B] mmCIF format, chain P [auth C] mmCIF format, chain V [auth D]	L [auth B], P [auth C], V [auth D]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain L [auth B] Focus chain P [auth C] Focus chain V [auth D] Interactions & Density Focus chain L [auth B] Focus chain P [auth C] Focus chain V [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.11 Å
R-Value Free: 0.225 (Depositor), 0.220 (DCC)
R-Value Work: 0.180 (Depositor), 0.180 (DCC)
R-Value Observed: 0.182 (Depositor)

Diffraction Data: https://doi.org/10.18430/m34du6

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 174.047	α = 90
b = 104.912	β = 96.89
c = 70.07	γ = 90

Software Package:

Software Name	Purpose
HKL-3000	data collection
HKL-3000	phasing
MOLREP	phasing
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2012-03-21

Deposition Author(s):

Center for Structural Genomics of Infectious Diseases (CSGID)

Revision History (Full details and data files)

Version 1.0: 2012-03-21
Type: Initial release
Version 1.1: 2015-10-21
Changes: Source and taxonomy
Version 1.2: 2023-09-13
Changes: Data collection, Database references, Derived calculations, Refinement description
Version 1.3: 2024-10-16
Changes: Structure summary