3F8X | pdb_00003f8x

Crystal structure of a putative delta-5-3-ketosteroid isomerase (eca2236) from pectobacterium atrosepticum scri1043 at 1.55 A resolution

PDB DOI: https://doi.org/10.2210/pdb3F8X/pdb

Classification: ISOMERASE
Organism(s): Pectobacterium atrosepticum SCRI1043
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2008-11-13 Released: 2008-12-09
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.55 Å
R-Value Free:
0.188 (Depositor), 0.200 (DCC)
R-Value Work:
0.158 (Depositor), 0.170 (DCC)
R-Value Observed:
0.160 (Depositor)

wwPDB Validation 3D Report Full Report

This is version 1.5 of the entry. See complete history.

Literature

Crystal structure of putative delta-5-3-ketosteroid isomerase (YP_050331.1) from ERWINIA CAROTOVORA ATROSEPTICA SCRI1043 at 1.55 A resolution

Joint Center for Structural Genomics (JCSG)

To be published.

Macromolecule Content

Total Structure Weight: 66.2 kDa
Atom Count: 5,096
Modeled Residue Count: 526
Deposited Residue Count: 592
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
putative delta-5-3-ketosteroid isomerase	A, B, C, D	148	Pectobacterium atrosepticum SCRI1043	Mutation(s): 0 Gene Names: ECA2236, YP_050331.1
UniProt
Find proteins for Q6D504 (Pectobacterium atrosepticum (strain SCRI 1043 / ATCC BAA-672)) Explore Q6D504 Go to UniProtKB: Q6D504
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q6D504
Sequence Annotations Expand
Reference Sequence

Small Molecules

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

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.55 Å
R-Value Free: 0.188 (Depositor), 0.200 (DCC)
R-Value Work: 0.158 (Depositor), 0.170 (DCC)
R-Value Observed: 0.160 (Depositor)

Diffraction Data: https://doi.org/10.18430/M33F8X

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 50.78	α = 79.41
b = 51.6	β = 79.74
c = 66.31	γ = 61.89

Software Package:

Software Name	Purpose
REFMAC	refinement
PHENIX	refinement
SHELX	phasing
MolProbity	model building
XSCALE	data scaling
PDB_EXTRACT	data extraction
XDS	data reduction
SHELXD	phasing
autoSHARP	phasing

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2008-12-09

Deposition Author(s):

Joint Center for Structural Genomics (JCSG)

Revision History (Full details and data files)

Version 1.0: 2008-12-09
Type: Initial release
Version 1.1: 2011-07-13
Changes: Advisory, Version format compliance
Version 1.2: 2017-10-25
Changes: Author supporting evidence, Refinement description
Version 1.3: 2019-07-24
Changes: Data collection, Derived calculations, Refinement description
Version 1.4: 2023-02-01
Changes: Database references
Version 1.5: 2024-11-20
Changes: Data collection, Structure summary

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.