4O9K | pdb_00004o9k

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)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.85 Å
R-Value Free:
0.189 (Depositor), 0.188 (DCC)
R-Value Work:
0.148 (Depositor), 0.148 (DCC)
R-Value Observed:
0.150 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

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.

Macromolecule Content

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

Macromolecules

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| 3D Structure

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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q60AU8
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CMK Query on CMK Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain E [auth B] MOL2 format, chain C [auth A] MOL2 format, chain E [auth B] mmCIF format, chain C [auth A] mmCIF format, chain E [auth B]	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		Interactions Focus chain C [auth A] Focus chain E [auth B] Interactions & Density Focus chain C [auth A] Focus chain E [auth B]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain D [auth B] MOL2 format, chain D [auth B] mmCIF format, chain D [auth B]	D [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain D [auth B] Interactions & Density Focus chain D [auth B]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE Query on 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), 0.188 (DCC)
R-Value Work: 0.148 (Depositor), 0.148 (DCC)
R-Value Observed: 0.150 (Depositor)

Diffraction Data:

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

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2014-01-22

Deposition Author(s):

New York Structural Genomics Research Consortium (NYSGRC)

Revision History (Full details and data files)

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