3HX8 | pdb_00003hx8

Crystal structure of putative ketosteroid isomerase (NP_103587.1) from Mesorhizobium loti at 1.45 A resolution

PDB DOI: https://doi.org/10.2210/pdb3HX8/pdb

Classification: ISOMERASE
Organism(s): Mesorhizobium loti
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2009-06-19 Released: 2009-07-07
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.45 Å
R-Value Free:
0.186 (Depositor), 0.191 (DCC)
R-Value Work:
0.147 (Depositor), 0.156 (DCC)
R-Value Observed:
0.149 (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 (NP_103587.1) from MESORHIZOBIUM LOTI at 1.45 A resolution

Joint Center for Structural Genomics (JCSG)

To be published.

Macromolecule Content

Total Structure Weight: 57.54 kDa
Atom Count: 4,787
Modeled Residue Count: 509
Deposited Residue Count: 516
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
putative ketosteroid isomerase	A, B, C, D	129	Mesorhizobium loti	Mutation(s): 0 Gene Names: mlr2180, NP_103587.1
UniProt
Find proteins for Q98IZ3 (Mesorhizobium japonicum (strain LMG 29417 / CECT 9101 / MAFF 303099)) Explore Q98IZ3 Go to UniProtKB: Q98IZ3
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q98IZ3
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PG4 Query on PG4 Download:Ideal Coordinates CCD File SDF format, chain J [auth C] SDF format, chain K [auth C] SDF format, chain M [auth D] MOL2 format, chain J [auth C] MOL2 format, chain K [auth C] MOL2 format, chain M [auth D] mmCIF format, chain J [auth C] mmCIF format, chain K [auth C] mmCIF format, chain M [auth D]	J [auth C], K [auth C], M [auth D]	TETRAETHYLENE GLYCOL C₈ H₁₈ O₅ UWHCKJMYHZGTIT-UHFFFAOYSA-N		Interactions Focus chain J [auth C] Focus chain K [auth C] Focus chain M [auth D] Interactions & Density Focus chain J [auth C] Focus chain K [auth C] Focus chain M [auth D]
IMD Query on IMD Download:Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain N [auth D] SDF format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain N [auth D] MOL2 format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain N [auth D] mmCIF format, chain F [auth A]	F [auth A], G [auth A], N [auth D]	IMIDAZOLE C₃ H₅ N₂ RAXXELZNTBOGNW-UHFFFAOYSA-O		Interactions Focus chain F [auth A] Focus chain G [auth A] Focus chain N [auth D] Interactions & Density Focus chain F [auth A] Focus chain G [auth A] Focus chain N [auth D]
UNL Query on UNL Download:Ideal Coordinates CCD File	E [auth A], H [auth B], I [auth C], L [auth D]	Unknown ligand RAXXELZNTBOGNW-UHFFFAOYSA-O		Interactions Focus chain E [auth A] Focus chain H [auth B] Focus chain I [auth C] Focus chain L [auth D] Interactions & Density Focus chain E [auth A] Focus chain H [auth B] Focus chain I [auth C] Focus chain L [auth D]

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: 1.45 Å
R-Value Free: 0.186 (Depositor), 0.191 (DCC)
R-Value Work: 0.147 (Depositor), 0.156 (DCC)
R-Value Observed: 0.149 (Depositor)

Diffraction Data:

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 48.336	α = 69.02
b = 55.111	β = 76.89
c = 56.862	γ = 64.83

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

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2009-07-07

Deposition Author(s):

Joint Center for Structural Genomics (JCSG)

Revision History (Full details and data files)

Version 1.0: 2009-07-07
Type: Initial release
Version 1.1: 2011-07-13
Changes: 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, Derived calculations
Version 1.5: 2024-10-16
Changes: Data collection, Structure summary