4WCZ | pdb_00004wcz

Crystal structure of a putative enoyl-CoA hydratase/isomerase from Novosphingobium aromaticivorans

PDB DOI: https://doi.org/10.2210/pdb4WCZ/pdb

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

Deposited: 2014-09-05 Released: 2014-12-03
Deposition Author(s): Tkaczuk, K.L., Cooper, D.R., Chapman, H.C., Niedzialkowska, E., Cymborowski, M.T., Hillerich, B.S., Stead, M., Ahmed, M., Hammonds, J., Bonanno, J., Seidel, R., Almo, S.C., Minor, W., New York Structural Genomics Research Consortium (NYSGRC)
Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.82 Å
R-Value Free:
0.193 (Depositor), 0.192 (DCC)
R-Value Work:
0.167 (Depositor), 0.167 (DCC)
R-Value Observed:
0.169 (Depositor)

wwPDB Validation 3D Report Full Report

This is version 1.6 of the entry. See complete history.

Literature

Crystal structure of a putative enoyl-CoA hydratase/isomerase from Novosphingobium aromaticivorans

Tkaczuk, K.L., Cooper, D.R., Chapman, H.C., Niedzialkowska, E., Cymborowski, M.T., Hillerich, B.S., Stead, M., Ahmed, M., Hammonds, J., Bonanno, J., Seidel, R., Almo, S.C., Minor, W., New York Structural Genomics Research Consortium (NYSGRC)

To be published.

Macromolecule Content

Total Structure Weight: 177.41 kDa
Atom Count: 12,671
Modeled Residue Count: 1,495
Deposited Residue Count: 1,632
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, C, D, E A, B, C, D, E, F	272	Novosphingobium aromaticivorans DSM 12444	Mutation(s): 0 Gene Names: Saro_3457
UniProt
Find proteins for A4XEF6 (Novosphingobium aromaticivorans (strain ATCC 700278 / DSM 12444 / CCUG 56034 / CIP 105152 / NBRC 16084 / F199)) Explore A4XEF6 Go to UniProtKB: A4XEF6
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A4XEF6
Sequence Annotations Expand
Reference Sequence

Small Molecules

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

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.82 Å
R-Value Free: 0.193 (Depositor), 0.192 (DCC)
R-Value Work: 0.167 (Depositor), 0.167 (DCC)
R-Value Observed: 0.169 (Depositor)

Diffraction Data:

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 81.636	α = 90
b = 128.469	β = 116.36
c = 84.467	γ = 90

Software Package:

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

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2014-12-03

Deposition Author(s):

New York Structural Genomics Research Consortium (NYSGRC)

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	NIH-5U54GM094662-04

Revision History (Full details and data files)

Version 1.0: 2014-12-03
Type: Initial release
Version 1.1: 2014-12-31
Changes: Database references, Structure summary
Version 1.2: 2017-09-27
Changes: Author supporting evidence, Derived calculations, Other, Refinement description, Source and taxonomy, Structure summary
Version 1.3: 2019-12-25
Changes: Author supporting evidence
Version 1.4: 2022-04-13
Changes: Database references, Refinement description, Structure summary
Version 1.5: 2023-12-27
Changes: Data collection
Version 1.6: 2024-10-16
Changes: Structure summary