3F4N | pdb_00003f4n

Crystal Structure of Pyridoxal Phosphate Biosynthetic Protein PdxJ from Yersinia pestis

PDB DOI: https://doi.org/10.2210/pdb3F4N/pdb

Classification: BIOSYNTHETIC PROTEIN, TRANSFERASE
Organism(s): Yersinia pestis
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2008-11-01 Released: 2008-11-25
Deposition Author(s): Kim, Y., Maltseva, N., Stam, J., Anderson, W.F., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.40 Å
R-Value Free:
0.266 (Depositor), 0.270 (DCC)
R-Value Work:
0.191 (Depositor), 0.190 (DCC)
R-Value Observed:
0.195 (Depositor)

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 Structure of Pyridoxal Phosphate Biosynthetic Protein PdxJ from Yersinia pestis

Kim, Y., Maltseva, N., Stam, J., Anderson, W.F., Joachimiak, A.

To be published.

Macromolecule Content

Total Structure Weight: 215.1 kDa
Atom Count: 15,591
Modeled Residue Count: 1,932
Deposited Residue Count: 1,968
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Pyridoxine 5'-phosphate synthase	A, B, C, D, E A, B, C, D, E, F, G, H	246	Yersinia pestis	Mutation(s): 0 Gene Names: pdxJ, y1300, YPO2930, YP_2525 EC: 2.6.99.2
UniProt
Find proteins for Q8ZCP4 (Yersinia pestis) Explore Q8ZCP4 Go to UniProtKB: Q8ZCP4
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q8ZCP4
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PXP Query on PXP Download Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain J [auth B] SDF format, chain K [auth C] SDF format, chain M [auth D] SDF format, chain N [auth E] SDF format, chain Q [auth F] SDF format, chain R [auth G] SDF format, chain S [auth H] MOL2 format, chain I [auth A] MOL2 format, chain J [auth B] MOL2 format, chain K [auth C] MOL2 format, chain M [auth D] MOL2 format, chain N [auth E] MOL2 format, chain Q [auth F] MOL2 format, chain R [auth G] MOL2 format, chain S [auth H] mmCIF format, chain I [auth A] mmCIF format, chain J [auth B] mmCIF format, chain K [auth C] mmCIF format, chain M [auth D] mmCIF format, chain N [auth E] mmCIF format, chain Q [auth F] mmCIF format, chain R [auth G] mmCIF format, chain S [auth H]	I [auth A] J [auth B] K [auth C] M [auth D] N [auth E] I [auth A], J [auth B], K [auth C], M [auth D], N [auth E], Q [auth F], R [auth G], S [auth H]	PYRIDOXINE-5'-PHOSPHATE C₈ H₁₂ N O₆ P WHOMFKWHIQZTHY-UHFFFAOYSA-N		Interactions Focus chain I [auth A] Focus chain J [auth B] Focus chain K [auth C] Focus chain M [auth D] Focus chain N [auth E] Focus chain Q [auth F] Focus chain R [auth G] Focus chain S [auth H] Interactions & Density Focus chain I [auth A] Focus chain J [auth B] Focus chain K [auth C] Focus chain M [auth D] Focus chain N [auth E] Focus chain Q [auth F] Focus chain R [auth G] Focus chain S [auth H]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain L [auth C] SDF format, chain O [auth E] SDF format, chain P [auth E] MOL2 format, chain L [auth C] MOL2 format, chain O [auth E] MOL2 format, chain P [auth E] mmCIF format, chain L [auth C] mmCIF format, chain O [auth E] mmCIF format, chain P [auth E]	L [auth C], O [auth E], P [auth E]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain L [auth C] Focus chain O [auth E] Focus chain P [auth E] Interactions & Density Focus chain L [auth C] Focus chain O [auth E] Focus chain P [auth E]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.40 Å
R-Value Free: 0.266 (Depositor), 0.270 (DCC)
R-Value Work: 0.191 (Depositor), 0.190 (DCC)
R-Value Observed: 0.195 (Depositor)

Diffraction Data: https://doi.org/10.18430/m33f4n

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 113.627	α = 90
b = 114.818	β = 90
c = 154.316	γ = 90

Software Package:

Software Name	Purpose
SBC-Collect	data collection
HKL-3000	data collection
BALBES	phasing
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2008-11-25

Deposition Author(s):

Center for Structural Genomics of Infectious Diseases (CSGID)

Revision History (Full details and data files)

Version 1.0: 2008-11-25
Type: Initial release
Version 1.1: 2011-07-13
Changes: Advisory, Refinement description, Version format compliance
Version 1.2: 2023-09-06
Changes: Data collection, Database references, Derived calculations, Refinement description

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Help and Resources

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Crystal Structure of Pyridoxal Phosphate Biosynthetic Protein PdxJ from Yersinia pestis

Crystal Structure of Pyridoxal Phosphate Biosynthetic Protein PdxJ from Yersinia pestis

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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Experimental Data

Structure Validation

Ligand Structure Quality Assessment

Deposition Data

Revision History (Full details and data files)

3F4N | pdb_00003f4n