4DGT

Crystal structure of PLP-bound putative aminotransferase from Clostridium difficile 630 crystallized with magnesium formate

PDB DOI: https://doi.org/10.2210/pdb4DGT/pdb

Classification: TRANSFERASE
Organism(s): Clostridioides difficile 630
Expression System: Escherichia coli BL21
Mutation(s): No

Deposited: 2012-01-26 Released: 2012-02-08
Deposition Author(s): Shabalin, I.G., Onopriyenko, O., Kudritska, M., Chruszcz, M., Grimshaw, S., Porebski, P.J., Cooper, D.R., Savchenko, A., Anderson, W.F., Minor, W., Center for Structural Genomics of Infectious Diseases (CSGID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.55 Å
R-Value Free: 0.181
R-Value Work: 0.147
R-Value Observed: 0.149

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

Crystal structures of putative aminotransferase from Clostridium difficile 630

Shabalin, I.G., Onopriyenko, O., Kudritska, M., Grimshaw, S., Chruszcz, M., Porebski, P.J., Cooper, D.R., Savchenko, A., Anderson, W.F., Minor, W.

To be published.

Macromolecule Content

Total Structure Weight: 91.03 kDa
Atom Count: 7,282
Modelled Residue Count: 774
Deposited Residue Count: 782
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative pyridoxal phosphate-dependent transferase	A, B	391	Clostridioides difficile 630	Mutation(s): 0 Gene Names: CD2733, CD630_27330 EC: 4.4.1.13
UniProt
Find proteins for Q183G9 (Clostridioides difficile (strain 630)) Explore Q183G9 Go to UniProtKB: Q183G9
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q183G9
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PLP Query on PLP Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain J [auth B] MOL2 format, chain C [auth A] MOL2 format, chain J [auth B] mmCIF format, chain C [auth A] mmCIF format, chain J [auth B]	C [auth A], J [auth B]	PYRIDOXAL-5'-PHOSPHATE C₈ H₁₀ N O₆ P NGVDGCNFYWLIFO-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain J [auth B] Interactions & Density Focus chain C [auth A] Focus chain J [auth B]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain M [auth B] SDF format, chain N [auth B] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain M [auth B] MOL2 format, chain N [auth B] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain M [auth B] mmCIF format, chain N [auth B]	G [auth A], H [auth A], M [auth B], N [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain G [auth A] Focus chain H [auth A] Focus chain M [auth B] Focus chain N [auth B] Interactions & Density Focus chain G [auth A] Focus chain H [auth A] Focus chain M [auth B] Focus chain N [auth B]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain I [auth A] SDF format, chain K [auth B] SDF format, chain L [auth B] SDF format, chain O [auth B] SDF format, chain P [auth B] SDF format, chain Q [auth B] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain I [auth A] MOL2 format, chain K [auth B] MOL2 format, chain L [auth B] MOL2 format, chain O [auth B] MOL2 format, chain P [auth B] MOL2 format, chain Q [auth B] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain I [auth A] mmCIF format, chain K [auth B] mmCIF format, chain L [auth B] mmCIF format, chain O [auth B] mmCIF format, chain P [auth B] mmCIF format, chain Q [auth B]	D [auth A] E [auth A] F [auth A] I [auth A] K [auth B] D [auth A], E [auth A], F [auth A], I [auth A], K [auth B], L [auth B], O [auth B], P [auth B], Q [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain I [auth A] Focus chain K [auth B] Focus chain L [auth B] Focus chain O [auth B] Focus chain P [auth B] Focus chain Q [auth B] Interactions & Density Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain I [auth A] Focus chain K [auth B] Focus chain L [auth B] Focus chain O [auth B] Focus chain P [auth B] Focus chain Q [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.55 Å
R-Value Free: 0.181
R-Value Work: 0.147
R-Value Observed: 0.149
Space Group: P 1 2₁ 1
Diffraction Data: https://doi.org/10.18430/M34DGT

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 78.744	α = 90
b = 55.624	β = 91.25
c = 79.133	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-3000	data collection
HKL-3000	data reduction
HKL-3000	data scaling
HKL-3000	phasing
MOLREP	phasing
CCP4	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2012-02-08

Deposition Author(s):

Center for Structural Genomics of Infectious Diseases (CSGID)

Revision History (Full details and data files)

Version 1.0: 2012-02-08
Type: Initial release
Version 1.1: 2022-04-13
Changes: Database references, Derived calculations, Structure summary
Version 1.2: 2023-09-13
Changes: Data collection, Refinement description