3BB9 | pdb_00003bb9

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 (Depositor), 0.230 (DCC)
R-Value Work:
0.175 (Depositor), 0.180 (DCC)
R-Value Observed:
0.178 (Depositor)

wwPDB Validation 3D Report Full Report

This is version 1.5 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
Modeled Residue Count: 743
Deposited Residue Count: 888
Unique protein chains: 1

Macromolecules

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| 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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% 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 P [auth F] SDF format, chain O [auth D] SDF format, chain N [auth C] SDF format, chain M [auth C] SDF format, chain L [auth C] SDF format, chain K [auth C] SDF format, chain J [auth B] SDF format, chain I [auth B] SDF format, chain H [auth B] SDF format, chain G [auth A] MOL2 format, chain P [auth F] MOL2 format, chain O [auth D] MOL2 format, chain N [auth C] MOL2 format, chain M [auth C] MOL2 format, chain L [auth C] MOL2 format, chain K [auth C] MOL2 format, chain J [auth B] MOL2 format, chain I [auth B] MOL2 format, chain H [auth B] MOL2 format, chain G [auth A] mmCIF format, chain P [auth F] mmCIF format, chain O [auth D] mmCIF format, chain N [auth C] mmCIF format, chain M [auth C] mmCIF format, chain L [auth C] mmCIF format, chain K [auth C] mmCIF format, chain J [auth B] mmCIF format, chain I [auth B] mmCIF format, chain H [auth B] mmCIF format, chain G [auth A]	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 (Depositor), 0.230 (DCC)
R-Value Work: 0.175 (Depositor), 0.180 (DCC)
R-Value Observed: 0.178 (Depositor)

Diffraction Data:

Space Group: P 2₁ 2₁ 2₁

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

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View more in-depth experimental data

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
Version 1.5: 2024-11-20
Changes: Data collection, Refinement description, Structure summary