6NQH | pdb_00006nqh

Xanthomonas citri Dephospho-PGM in complex with xylose-1-phosphate

• PDB DOI: https://doi.org/10.2210/pdb6NQH/pdb

• Classification: ISOMERASE
• Organism(s): Xanthomonas citri pv. citri str. 306
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2019-01-21 Released: 2020-01-29 
• Deposition Author(s): Stiers, K.M., Beamer, L.J.
• Funding Organization(s): National Science Foundation (NSF, United States)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.45 Å
• R-Value Free: 
  0.215 (Depositor), 0.210 (DCC) 
• R-Value Work: 
  0.177 (Depositor), 0.180 (DCC) 
• R-Value Observed: 
  0.179 (Depositor) 

Starting Model: experimental

Literature

Substate dynamics of the XcPGM reaction mechanism

Stiers, K.M., Beamer, L.J.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: SAXS

Macromolecule Content 

• Total Structure Weight: 51.84 kDa 
• Atom Count: 3,892 
• Modeled Residue Count: 448 
• Deposited Residue Count: 468 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Phosphoglucomutase	A	468	Xanthomonas citri pv. citri str. 306	Mutation(s): 0  Gene Names: xanA, XAC3579

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
X1P	C [auth A], D [auth A]	1-O-phosphono-alpha-D-xylopyranose C5 H11 O8 P ILXHFXFPPZGENN-KKQCNMDGSA-N
MG	B [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.45 Å
• R-Value Free:  0.215 (Depositor), 0.210 (DCC) 
• R-Value Work:  0.177 (Depositor), 0.180 (DCC) 
• R-Value Observed: 0.179 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 43.863	α = 90
b = 54.626	β = 90
c = 173.359	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2020-01-29 
Deposition Author(s): Stiers, K.M., Beamer, L.J.

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Funding Organization	Location	Grant Number
National Science Foundation (NSF, United States)	United States	MCB-1409898

Revision History  

• Version 1.0: 2020-01-29
  Type: Initial release
  
• Version 1.1: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Derived calculations, Structure summary
• Version 1.2: 2023-10-11
  Changes: Data collection, Database references, Refinement description, Structure summary