3B85 | pdb_00003b85

Crystal structure of predicted phosphate starvation-induced ATPase PhoH2 from Corynebacterium glutamicum

• PDB DOI: https://doi.org/10.2210/pdb3B85/pdb

• Classification: HYDROLASE
• Organism(s): Corynebacterium glutamicum ATCC 13032
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2007-10-31 Released: 2007-12-18 
• Deposition Author(s): Cuff, M.E., Wu, R., Gu, M., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.35 Å
• R-Value Free: 
  0.234 (Depositor), 0.209 (DCC) 
• R-Value Work: 
  0.180 (Depositor), 0.191 (DCC) 
• R-Value Observed: 
  0.183 (Depositor) 

Literature

A structure of predicted phosphate starvation-induced ATPase PhoH2 from Corynebacterium glutamicum.

Cuff, M.E., Wu, R., Gu, M., Joachimiak, A.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C6  (Explore in 3D)
Global Stoichiometry: Homo 6-mer - A6 

Biological assembly 1 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 46.97 kDa 
• Atom Count: 3,024 
• Modeled Residue Count: 374 
• Deposited Residue Count: 416 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Phosphate starvation-inducible protein	A, B	208	Corynebacterium glutamicum ATCC 13032	Mutation(s): 0  Gene Names: phoH2, cg2513
UniProt
Find proteins for Q8NNB6 (Corynebacterium glutamicum (strain ATCC 13032 / DSM 20300 / JCM 1318 / BCRC 11384 / CCUG 27702 / LMG 3730 / NBRC 12168 / NCIMB 10025 / NRRL B-2784 / 534)) Explore Q8NNB6  Go to UniProtKB:  Q8NNB6

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	C [auth A], D [auth A], E [auth A], F [auth A], G [auth A], H [auth B], I [auth B], J [auth B], K [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A, B	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.35 Å
• R-Value Free:  0.234 (Depositor), 0.209 (DCC) 
• R-Value Work:  0.180 (Depositor), 0.191 (DCC) 
• R-Value Observed: 0.183 (Depositor) 

Space Group: P 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 98.668	α = 90
b = 98.668	β = 90
c = 36.675	γ = 120

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
MLPHARE	phasing
DM	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
SBC-Collect	data collection
HKL-3000	data reduction
HKL-3000	data scaling
HKL-3000	phasing
SHELXD	phasing
SHELXE	model building
SOLVE	phasing
RESOLVE	phasing
ARP/wARP	model building
CCP4	phasing
O	model building
Coot	model building

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-12-18 
Deposition Author(s): Cuff, M.E., Wu, R., Gu, M., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Revision History  

• Version 1.0: 2007-12-18
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.2: 2017-10-25
  Changes: Refinement description
• Version 1.3: 2024-11-20
  Changes: Data collection, Database references, Derived calculations, Structure summary