2RD9

Crystal structure of a putative yfit-like metal-dependent hydrolase (bh0186) from bacillus halodurans c-125 at 2.30 A resolution

PDB DOI: https://doi.org/10.2210/pdb2RD9/pdb

Classification: HYDROLASE
Organism(s): Halalkalibacterium halodurans C-125
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2007-09-21 Released: 2007-10-09
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free: 0.201
R-Value Work: 0.152
R-Value Observed: 0.155

wwPDB Validation 3D Report Full Report

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

Literature

Crystal structure of YfiT-like putative metal-dependent hydrolase (NP_241052.1) from Bacillus halodurans at 2.30 A resolution

Joint Center for Structural Genomics (JCSG)

To be published.

Macromolecule Content

Total Structure Weight: 92.79 kDa
Atom Count: 6,934
Modelled Residue Count: 748
Deposited Residue Count: 772
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
BH0186 protein	A, B, C, D	193	Halalkalibacterium halodurans C-125	Mutation(s): 0 Gene Names: NP_241052.1, BH0186
UniProt
Find proteins for Q9KGB8 (Halalkalibacterium halodurans (strain ATCC BAA-125 / DSM 18197 / FERM 7344 / JCM 9153 / C-125)) Explore Q9KGB8 Go to UniProtKB: Q9KGB8
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9KGB8
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain K [auth A] SDF format, chain M [auth B] SDF format, chain Q [auth C] SDF format, chain S [auth D] SDF format, chain T [auth D] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain M [auth B] MOL2 format, chain Q [auth C] MOL2 format, chain S [auth D] MOL2 format, chain T [auth D]	I [auth A] J [auth A] K [auth A] M [auth B] Q [auth C] I [auth A], J [auth A], K [auth A], M [auth B], Q [auth C], S [auth D], T [auth D]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain M [auth B] Focus chain Q [auth C] Focus chain S [auth D] Focus chain T [auth D] Interactions & Density Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain M [auth B] Focus chain Q [auth C] Focus chain S [auth D] Focus chain T [auth D]
IMD Query on IMD Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain O [auth C] SDF format, chain P [auth C] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain O [auth C] MOL2 format, chain P [auth C]	F [auth A], G [auth A], H [auth A], O [auth C], P [auth C]	IMIDAZOLE C₃ H₅ N₂ RAXXELZNTBOGNW-UHFFFAOYSA-O		Interactions Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain O [auth C] Focus chain P [auth C] Interactions & Density Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain O [auth C] Focus chain P [auth C]
NI Query on NI Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain L [auth B] SDF format, chain N [auth C] SDF format, chain R [auth D] MOL2 format, chain E [auth A] MOL2 format, chain L [auth B] MOL2 format, chain N [auth C] MOL2 format, chain R [auth D]	E [auth A], L [auth B], N [auth C], R [auth D]	NICKEL (II) ION Ni VEQPNABPJHWNSG-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain L [auth B] Focus chain N [auth C] Focus chain R [auth D] Interactions & Density Focus chain E [auth A] Focus chain L [auth B] Focus chain N [auth C] Focus chain R [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: 2.30 Å
R-Value Free: 0.201
R-Value Work: 0.152
R-Value Observed: 0.155
Space Group: P 2₁ 3
Diffraction Data: https://doi.org/10.18430/M32RD9

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 147.33	α = 90
b = 147.33	β = 90
c = 147.33	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PHENIX	refinement
SHELX	phasing
MolProbity	model building
XSCALE	data scaling
PDB_EXTRACT	data extraction
MAR345	data collection
XDS	data reduction
autoSHARP	phasing

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2007-10-09

Deposition Author(s):

Joint Center for Structural Genomics (JCSG)

Revision History (Full details and data files)

Version 1.0: 2007-10-09
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: 2023-01-25
Changes: Database references, Derived calculations

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Validate Data

Deposit Data

Help and Resources

2RD9

Crystal structure of a putative yfit-like metal-dependent hydrolase (bh0186) from bacillus halodurans c-125 at 2.30 A resolution

Crystal structure of YfiT-like putative metal-dependent hydrolase (NP_241052.1) from Bacillus halodurans at 2.30 A resolution

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

Expand

Experimental Data

Structure Validation

Deposition Data

Revision History (Full details and data files)