3BB9

Crystal structure of a putative ketosteroid isomerase (sfri_1973) from shewanella frigidimarina ncimb 400 at 1.80 A resolution

PDB DOI: https://doi.org/10.2210/pdb3BB9/pdb

Classification: UNKNOWN FUNCTION
Organism(s): Shewanella frigidimarina NCIMB 400
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2007-11-09 Released: 2007-11-20
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free: 0.228
R-Value Work: 0.175
R-Value Observed: 0.178

wwPDB Validation 3D Report Full Report

This is version 1.4 of the entry. See complete history.

Literature

Crystal structure of putative ketosteroid isomerase (YP_750657.1) from Shewanella frigidimarina NCIMB 400 at 1.80 A resolution

Joint Center for Structural Genomics (JCSG)

To be published.

Macromolecule Content

Total Structure Weight: 98.97 kDa
Atom Count: 6,430
Modelled Residue Count: 743
Deposited Residue Count: 888
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative orphan protein	A, B, C, D, E A, B, C, D, E, F	148	Shewanella frigidimarina NCIMB 400	Mutation(s): 0 Gene Names: YP_750657.1, Sfri_1973
UniProt
Find proteins for Q082J6 (Shewanella frigidimarina (strain NCIMB 400)) Explore Q082J6 Go to UniProtKB: Q082J6
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q082J6
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain H [auth B] SDF format, chain I [auth B] SDF format, chain J [auth B] SDF format, chain K [auth C] SDF format, chain L [auth C] SDF format, chain M [auth C] SDF format, chain N [auth C] SDF format, chain O [auth D] SDF format, chain P [auth F] MOL2 format, chain G [auth A] MOL2 format, chain H [auth B] MOL2 format, chain I [auth B] MOL2 format, chain J [auth B] MOL2 format, chain K [auth C] MOL2 format, chain L [auth C] MOL2 format, chain M [auth C] MOL2 format, chain N [auth C] MOL2 format, chain O [auth D] MOL2 format, chain P [auth F]	G [auth A] H [auth B] I [auth B] J [auth B] K [auth C] G [auth A], H [auth B], I [auth B], J [auth B], K [auth C], L [auth C], M [auth C], N [auth C], O [auth D], P [auth F]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain H [auth B] Focus chain I [auth B] Focus chain J [auth B] Focus chain K [auth C] Focus chain L [auth C] Focus chain M [auth C] Focus chain N [auth C] Focus chain O [auth D] Focus chain P [auth F] Interactions & Density Focus chain G [auth A] Focus chain H [auth B] Focus chain I [auth B] Focus chain J [auth B] Focus chain K [auth C] Focus chain L [auth C] Focus chain M [auth C] Focus chain N [auth C] Focus chain O [auth D] Focus chain P [auth F]

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

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free: 0.228
R-Value Work: 0.175
R-Value Observed: 0.178
Space Group: P 2₁ 2₁ 2₁
Diffraction Data: https://doi.org/10.18430/M33BB9

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 42.558	α = 90
b = 113.82	β = 90
c = 137.132	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PHENIX	refinement
SHELX	phasing
MolProbity	model building
SCALA	data scaling
PDB_EXTRACT	data extraction
ADSC	data collection
MOSFLM	data reduction
SHELXD	phasing
SHARP	phasing

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2007-11-20

Deposition Author(s):

Joint Center for Structural Genomics (JCSG)

Revision History (Full details and data files)

Version 1.0: 2007-11-20
Type: Initial release
Version 1.1: 2011-07-13
Changes: Advisory, Source and taxonomy, 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: 2023-01-25
Changes: Database references, Derived calculations

Prepare Data

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Help and Resources

3BB9

Crystal structure of a putative ketosteroid isomerase (sfri_1973) from shewanella frigidimarina ncimb 400 at 1.80 A resolution

Crystal structure of putative ketosteroid isomerase (YP_750657.1) from Shewanella frigidimarina NCIMB 400 at 1.80 A resolution

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

Expand

Experimental Data

Structure Validation

Deposition Data

Revision History (Full details and data files)