4HJH | pdb_00004hjh

Iodide SAD phased crystal structure of a phosphoglucomutase from Brucella melitensis complexed with glucose-6-phosphate

• PDB DOI: https://doi.org/10.2210/pdb4HJH/pdb

• Classification: ISOMERASE
• Organism(s): Brucella melitensis bv. 1 str. 16M
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2012-10-12 Released: 2012-11-21 
• Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 
  0.209 (Depositor), 0.210 (DCC) 
• R-Value Work: 
  0.174 (Depositor), 0.181 (DCC) 
• R-Value Observed: 
  0.175 (Depositor) 

Literature

Iodide SAD phased crystal structure of a phosphoglucomutase from Brucella melitensis complexed with glucose-6-phosphate

Fairman, J.W., Craig, T.K., Staker, B.L.

To be published.

Biological Assembly 1  

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

Biological assembly 1 generated by PISA (software)

Biological Assembly 2  

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

Biological assembly 2 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 112.67 kDa 
• Atom Count: 7,469 
• Modeled Residue Count: 931 
• Deposited Residue Count: 962 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Phosphomannomutase	A, B	481	Brucella melitensis bv. 1 str. 16M	Mutation(s): 0  Gene Names: BAWG_1686 EC: 5.4.2.8

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
G6Q	IC [auth B], TA [auth A]	GLUCOSE-6-PHOSPHATE C6 H13 O9 P VFRROHXSMXFLSN-SLPGGIOYSA-N
IOD	AA [auth A], AC [auth B], BA [auth A], BC [auth B], C [auth A], CA [auth A], CB [auth B], CC [auth B], D [auth A], DA [auth A], DB [auth B], DC [auth B], E [auth A], EA [auth A], EB [auth B], EC [auth B], F [auth A], FA [auth A], FB [auth B], FC [auth B], G [auth A], GA [auth A], GB [auth B], GC [auth B], H [auth A], HA [auth A], HB [auth B], HC [auth B], I [auth A], IA [auth A], IB [auth B], J [auth A], JA [auth A], JB [auth B], K [auth A], KA [auth A], KB [auth B], L [auth A], LA [auth A], LB [auth B], M [auth A], MA [auth A], MB [auth B], N [auth A], NA [auth A], NB [auth B], O [auth A], OA [auth A], OB [auth B], P [auth A], PA [auth A], PB [auth B], Q [auth A], QA [auth A], QB [auth B], R [auth A], RA [auth A], RB [auth B], S [auth A], SA [auth A], SB [auth B], T [auth A], TB [auth B], U [auth A], UB [auth B], V [auth A], VB [auth B], W [auth A], WB [auth B], X [auth A], XB [auth B], Y [auth A], YB [auth B], Z [auth A], ZB [auth B]	IODIDE ION I XMBWDFGMSWQBCA-UHFFFAOYSA-M
EDO	AB [auth A], JC [auth B], UA [auth A], VA [auth A], WA [auth A], XA [auth A], YA [auth A], ZA [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
MG	BB [auth A], KC [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
SEP	A, B	L-PEPTIDE LINKING	C3 H8 N O6 P		SER

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free:  0.209 (Depositor), 0.210 (DCC) 
• R-Value Work:  0.174 (Depositor), 0.181 (DCC) 
• R-Value Observed: 0.175 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M34HJH

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 61.95	α = 90
b = 55.98	β = 92.18
c = 131.67	γ = 90

Software Package:

Software Name	Purpose
XSCALE	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-11-21 
Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Revision History  

• Version 1.0: 2012-11-21
  Type: Initial release
  
• Version 1.1: 2017-09-20
  Changes: Data collection
• Version 1.2: 2017-10-11
  Changes: Data collection
• Version 1.3: 2024-11-27
  Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary