4KD6 | pdb_00004kd6

Crystal structure of a Enoyl-CoA hydratase/isomerase from Burkholderia graminis C4D1M

PDB DOI: https://doi.org/10.2210/pdb4KD6/pdb

Classification: ISOMERASE
Organism(s): Paraburkholderia graminis C4D1M
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2013-04-24 Released: 2013-07-24
Deposition Author(s): Kumaran, D., Chamala, S., Evans, B., Foti, R., Gizzi, A., Hillerich, B., Kar, A., Lafleur, J., Seidel, R., Villigas, G., Zencheck, W., Al Obaidi, N., Almo, S.C., Swaminathan, S., New York Structural Genomics Research Consortium (NYSGRC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.25 Å
R-Value Free:
0.230 (Depositor), 0.231 (DCC)
R-Value Work:
0.179 (Depositor), 0.180 (DCC)
R-Value Observed:
0.182 (Depositor)

wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

Literature

Crystal structure of a Enoyl-CoA hydratase/isomerase from Burkholderia graminis C4D1M

Kumaran, D., Almo, S.C., Swaminathan, S.

To be published.

Macromolecule Content

Total Structure Weight: 31.45 kDa
Atom Count: 1,746
Modeled Residue Count: 215
Deposited Residue Count: 275
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Enoyl-CoA hydratase/isomerase	A	275	Paraburkholderia graminis C4D1M	Mutation(s): 0 Gene Names: BgramDRAFT_6579
UniProt
Find proteins for B1GB42 (Paraburkholderia graminis (strain ATCC 700544 / DSM 17151 / LMG 18924 / NCIMB 13744 / C4D1M)) Explore B1GB42 Go to UniProtKB: B1GB42
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	B1GB42
Sequence Annotations Expand
Reference Sequence

Small Molecules

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

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.25 Å
R-Value Free: 0.230 (Depositor), 0.231 (DCC)
R-Value Work: 0.179 (Depositor), 0.180 (DCC)
R-Value Observed: 0.182 (Depositor)

Space Group: P 6₃

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 118.481	α = 90
b = 118.481	β = 90
c = 38.932	γ = 120

Software Package:

Software Name	Purpose
CBASS	data collection
SHELXD	phasing
SHELXE	model building
ARP/wARP	model building
Coot	model building
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2013-07-24

Deposition Author(s):

New York Structural Genomics Research Consortium (NYSGRC)

Revision History (Full details and data files)

Version 1.0: 2013-07-24
Type: Initial release
Version 1.1: 2024-10-30
Changes: Data collection, Database references, Derived calculations, Structure summary