4KVH | pdb_00004kvh

Crystal structure of ketosteroid isomerase fold protein Hmuk_0747

PDB DOI: https://doi.org/10.2210/pdb4KVH/pdb

Classification: UNKNOWN FUNCTION
Organism(s): Halomicrobium mukohataei DSM 12286
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2013-05-22 Released: 2013-06-12
Deposition Author(s): Chang, C., Holowicki, J., Bearden, J., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.61 Å
R-Value Free:
0.181 (Depositor), 0.179 (DCC)
R-Value Work:
0.156 (Depositor), 0.156 (DCC)
R-Value Observed:
0.158 (Depositor)

wwPDB Validation 3D Report Full Report

This is version 1.2 of the entry. See complete history.

Literature

Crystal structure of ketosteroid isomerase fold protein Hmuk_0747

Chang, C., Holowicki, J., Bearden, J., Joachimiak, A.

To be published.

Macromolecule Content

Total Structure Weight: 14.32 kDa
Atom Count: 1,138
Modeled Residue Count: 111
Deposited Residue Count: 113
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ketosteroid isomerase fold protein Hmuk_0747	A	113	Halomicrobium mukohataei DSM 12286	Mutation(s): 0 Gene Names: Hmuk_0747
UniProt
Find proteins for C7NZX0 (Halomicrobium mukohataei (strain ATCC 700874 / DSM 12286 / JCM 9738 / NCIMB 13541)) Explore C7NZX0 Go to UniProtKB: C7NZX0
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	C7NZX0
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CAC Query on CAC Download:Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	CACODYLATE ION C₂ H₆ As O₂ OGGXGZAMXPVRFZ-UHFFFAOYSA-M		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
BR Query on BR Download:Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain N [auth A] SDF format, chain R [auth A] SDF format, chain Q [auth A] SDF format, chain P [auth A] SDF format, chain O [auth A] SDF format, chain M [auth A] SDF format, chain L [auth A] SDF format, chain K [auth A] SDF format, chain J [auth A] SDF format, chain I [auth A] SDF format, chain H [auth A] SDF format, chain F [auth A] SDF format, chain E [auth A] SDF format, chain D [auth A] MOL2 format, chain G [auth A] MOL2 format, chain N [auth A] MOL2 format, chain R [auth A] MOL2 format, chain Q [auth A] MOL2 format, chain P [auth A] MOL2 format, chain O [auth A] MOL2 format, chain M [auth A] MOL2 format, chain L [auth A] MOL2 format, chain K [auth A] MOL2 format, chain J [auth A] MOL2 format, chain I [auth A] MOL2 format, chain H [auth A] MOL2 format, chain F [auth A] MOL2 format, chain E [auth A] MOL2 format, chain D [auth A] mmCIF format, chain G [auth A] mmCIF format, chain N [auth A] mmCIF format, chain R [auth A] mmCIF format, chain Q [auth A] mmCIF format, chain P [auth A] mmCIF format, chain O [auth A] mmCIF format, chain M [auth A] mmCIF format, chain L [auth A] mmCIF format, chain K [auth A] mmCIF format, chain J [auth A] mmCIF format, chain I [auth A] mmCIF format, chain H [auth A] mmCIF format, chain F [auth A] mmCIF format, chain E [auth A] mmCIF format, chain D [auth A]	D [auth A] E [auth A] F [auth A] G [auth A] H [auth A] D [auth A], E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], J [auth A], K [auth A], L [auth A], M [auth A], N [auth A], O [auth A], P [auth A], Q [auth A], R [auth A]	BROMIDE ION Br CPELXLSAUQHCOX-UHFFFAOYSA-M		Interactions Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A] Focus chain P [auth A] Focus chain Q [auth A] Focus chain R [auth A] Interactions & Density Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A] Focus chain P [auth A] Focus chain Q [auth A] Focus chain R [auth A]
FMT Query on FMT Download:Ideal Coordinates CCD File SDF format, chain S [auth A] MOL2 format, chain S [auth A] mmCIF format, chain S [auth A]	S [auth A]	FORMIC ACID C H₂ O₂ BDAGIHXWWSANSR-UHFFFAOYSA-N		Interactions Focus chain S [auth A] Interactions & Density Focus chain S [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.61 Å
R-Value Free: 0.181 (Depositor), 0.179 (DCC)
R-Value Work: 0.156 (Depositor), 0.156 (DCC)
R-Value Observed: 0.158 (Depositor)

Space Group: P 6₃ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 91.785	α = 90
b = 91.785	β = 90
c = 77.963	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
SBC-Collect	data collection
HKL-3000	data reduction
HKL-3000	data scaling
HKL-3000	phasing
MLPHARE	phasing
DM	phasing
SHELXDE	phasing
ARP/wARP	model building
RESOLVE	phasing
Coot	model building

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2013-06-12

Deposition Author(s):

Midwest Center for Structural Genomics (MCSG)

Revision History (Full details and data files)

Version 1.0: 2013-06-12
Type: Initial release
Version 1.1: 2017-11-15
Changes: Refinement description
Version 1.2: 2024-02-28
Changes: Data collection, Database references, Derived calculations