4JYJ | pdb_00004jyj

Crystal Structure of putative enoyl-CoA hydratase/isomerase from Novosphingobium aromaticivorans DSM 12444

PDB DOI: https://doi.org/10.2210/pdb4JYJ/pdb

Classification: ISOMERASE
Organism(s): Novosphingobium aromaticivorans DSM 12444
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2013-03-29 Released: 2013-05-29
Deposition Author(s): Cooper, D.R., Porebski, P.J., Domagalski, M.J., Ahmed, M., Stead, M., Hillerich, B., Seidel, R., Zimmerman, M., Bonanno, J.B., Almo, S.C., Minor, W., New York Structural Genomics Research Consortium (NYSGRC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free:
0.207 (Depositor), 0.211 (DCC)
R-Value Work:
0.154 (Depositor), 0.162 (DCC)
R-Value Observed:
0.157 (Depositor)

wwPDB Validation 3D Report Full Report

This is version 1.3 of the entry. See complete history.

Literature

Crystal Structure of putative enoyl-CoA hydratase/isomerase from Novosphingobium aromaticivorans DSM 12444

Cooper, D.R., Porebski, P.J., Domagalski, M.J., Ahmed, M., Stead, M., Hillerich, B., Seidel, R., Zimmerman, M., Bonanno, J.B., Almo, S.C., Minor, W., New York Structural Genomics Research Consortium (NYSGRC)

To be published.

Macromolecule Content

Total Structure Weight: 66.02 kDa
Atom Count: 4,195
Modeled Residue Count: 538
Deposited Residue Count: 604
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Enoyl-CoA hydratase/isomerase	A, B	302	Novosphingobium aromaticivorans DSM 12444	Mutation(s): 0 Gene Names: Saro_0518
UniProt
Find proteins for Q2GB08 (Novosphingobium aromaticivorans (strain ATCC 700278 / DSM 12444 / CCUG 56034 / CIP 105152 / NBRC 16084 / F199)) Explore Q2GB08 Go to UniProtKB: Q2GB08
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q2GB08
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
UNL Query on UNL Download:Ideal Coordinates CCD File	C [auth A], D [auth B]	Unknown ligand		Interactions Focus chain C [auth A] Focus chain D [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth B]

Modified Residues 1 Unique
ID	Chains	Modified Residue	Modification Type	Formula	2D Diagram
MSE Query on MSE	A, B	MET	Selenomethionine	C₅ H₁₁ N O₂ Se

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free: 0.207 (Depositor), 0.211 (DCC)
R-Value Work: 0.154 (Depositor), 0.162 (DCC)
R-Value Observed: 0.157 (Depositor)

Diffraction Data:

Space Group: P 2₁ 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 112.697	α = 90
b = 112.697	β = 90
c = 112.697	γ = 90

Software Package:

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

Structure Validation

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View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2013-05-29

Deposition Author(s):

New York Structural Genomics Research Consortium (NYSGRC)

Revision History (Full details and data files)

Version 1.0: 2013-05-29
Type: Initial release
Version 1.1: 2017-11-15
Changes: Refinement description
Version 1.2: 2022-04-13
Changes: Database references, Derived calculations, Structure summary
Version 1.3: 2024-11-20
Changes: Data collection, Refinement description, Structure summary