3N4D | pdb_00003n4d

Crystal structure of Cg10062 inactivated by(R)-oxirane-2-carboxylate

PDB DOI: https://doi.org/10.2210/pdb3N4D/pdb

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

Deposited: 2010-05-21 Released: 2011-06-01
Deposition Author(s): Guo, Y., Robertson, B.A., Hackert, M.L., Whitman, C.P.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.54 Å
R-Value Free:
0.243 (Depositor), 0.244 (DCC)
R-Value Work:
0.223 (Depositor), 0.224 (DCC)
R-Value Observed:
0.224 (Depositor)

Starting Model: experimental
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This is version 1.3 of the entry. See complete history.

Literature

Crystal Structures of the Native and Inactivated Cg10062, a cis-3-Chloroacrylic Acid Dehalogenase from Corynebacterium glutamicum: Implications for the Evolution of cis-3-Chloroacrylic Acid Dehalogenase Activity in the Tautomerase Superfamily

Guo, Y., Robertson, B.A., J Poelarends, G., Thunnissen, A.-M.W.H., Hackert, M.L., Whitman, C.P., Dijkstra, B.W.

To be published.

Macromolecule Content

Total Structure Weight: 154.83 kDa
Atom Count: 11,026
Modeled Residue Count: 1,301
Deposited Residue Count: 1,332
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative tautomerase	A, B, C, D, E A, B, C, D, E, F, G, H, I	148	Corynebacterium glutamicum	Mutation(s): 0 Gene Names: cg0081, Cg10062, Cgl0062 EC: 3.8.1
UniProt
Find proteins for Q8NU77 (Corynebacterium glutamicum (strain ATCC 13032 / DSM 20300 / JCM 1318 / BCRC 11384 / CCUG 27702 / LMG 3730 / NBRC 12168 / NCIMB 10025 / NRRL B-2784 / 534)) Explore Q8NU77 Go to UniProtKB: Q8NU77
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q8NU77
Sequence Annotations Expand
Reference Sequence

Small Molecules

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
PR4 Query on PR4	A, B, C, D, E A, B, C, D, E, F, G, H, I	L-PEPTIDE LINKING	C₈ H₁₃ N O₅		PRO

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.54 Å
R-Value Free: 0.243 (Depositor), 0.244 (DCC)
R-Value Work: 0.223 (Depositor), 0.224 (DCC)
R-Value Observed: 0.224 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 57.099	α = 90
b = 131.002	β = 90
c = 179.393	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
CrystalClear	data collection
HKL-2000	data reduction
HKL-2000	data scaling
MOLREP	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2011-06-01

Deposition Author(s):

Robertson, B.A.

Revision History (Full details and data files)

Version 1.0: 2011-06-01
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2018-01-24
Changes: Database references
Version 1.3: 2023-09-06
Changes: Data collection, Database references, Derived calculations, Refinement description

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.