4O9K

Crystal structure of the CBS pair of a putative D-arabinose 5-phosphate isomerase from Methylococcus capsulatus in complex with CMP-Kdo

• PDB DOI: https://doi.org/10.2210/pdb4O9K/pdb

• Classification: ISOMERASE
• Organism(s): Methylococcus capsulatus str. Bath
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2014-01-02 Released: 2014-01-22 
• Deposition Author(s): Shabalin, I.G., Cooper, D.R., Shumilin, I.A., Zimmerman, M.D., Majorek, K.A., Hammonds, J., Hillerich, B.S., Nawar, A., Bonanno, J., Seidel, R., Almo, S.C., Minor, W., New York Structural Genomics Research Consortium (NYSGRC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free: 
  0.189 (Depositor), 0.190 (DCC) 
• R-Value Work: 
  0.148 (Depositor), 0.150 (DCC) 
• R-Value Observed: 
  0.150 (Depositor) 

Literature

Crystal structure and kinetic properties of D-arabinose 5-phosphate isomerase from Methylococcus capsulatus

Shabalin, I.G., Cooper, D.R., Shumilin, I.A., Zimmerman, M.D., Majorek, K.A., Hammonds, J., Hillerich, B.S., Nawar, A., Bonanno, J., Seidel, R., Almo, S.C., Minor, W.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Macromolecule Content

• Total Structure Weight: 29.75 kDa 
• Atom Count: 2,220 
• Modelled Residue Count: 258 
• Deposited Residue Count: 260 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Arabinose 5-phosphate isomerase	A, B	130	Methylococcus capsulatus str. Bath	Mutation(s): 0  Gene Names: Locus tag MCA0746, MCA0746 EC: 5.3.1.13
UniProt
Find proteins for Q60AU8 (Methylococcus capsulatus (strain ATCC 33009 / NCIMB 11132 / Bath)) Explore Q60AU8  Go to UniProtKB:  Q60AU8

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CMK	C [auth A], E [auth B]	CYTIDINE 5'-MONOPHOSPHATE 3-DEOXY-BETA-D-GULO-OCT-2-ULO-PYRANOSONIC ACID C17 H26 N3 O15 P YWWJKULNWGRYAS-UOVSKDHASA-N
GOL	D [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

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: 1.85 Å
• R-Value Free:  0.189 (Depositor), 0.190 (DCC) 
• R-Value Work:  0.148 (Depositor), 0.150 (DCC) 
• R-Value Observed: 0.150 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M35C7X

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 45.151	α = 90
b = 62.408	β = 90
c = 75.664	γ = 90

Software Package:

Software Name	Purpose
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-3000	data collection
HKL-3000	data reduction
HKL-3000	data scaling
SHELX	phasing
MLPHARE	phasing
HKL-3000	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-01-22 
Deposition Author(s): Shabalin, I.G., Cooper, D.R., Shumilin, I.A., Zimmerman, M.D., Majorek, K.A., Hammonds, J., Hillerich, B.S., Nawar, A., Bonanno, J., Seidel, R., Almo, S.C., Minor, W., New York Structural Genomics Research Consortium (NYSGRC)

Revision History  

• Version 1.0: 2014-01-22
  Type: Initial release
  
• Version 1.1: 2022-04-13
  Changes: Database references, Derived calculations, Structure summary
• Version 1.2: 2024-10-09
  Changes: Data collection, Refinement description, Structure summary