2QEE | pdb_00002qee

Crystal structure of putative amidohydrolase BH0493 from Bacillus halodurans C-125

PDB DOI: https://doi.org/10.2210/pdb2QEE/pdb

Classification: HYDROLASE
Organism(s): Halalkalibacterium halodurans C-125
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2007-06-25 Released: 2007-07-24
Deposition Author(s): Malashkevich, V.N., Toro, R., Wasserman, S., Sauder, J.M., Burley, S.K., Almo, S.C., New York SGX Research Center for Structural Genomics (NYSGXRC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.65 Å
R-Value Free:
0.224 (Depositor), 0.223 (DCC)
R-Value Work:
0.187 (Depositor), 0.187 (DCC)
R-Value Observed:
0.189 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

This is version 1.6 of the entry. See complete history.

Literature

Crystal structure of putative amidohydrolase BH0493 from Bacillus halodurans C-125.

Malashkevich, V.N., Toro, R., Wasserman, S., Sauder, J.M., Burley, S.K., Almo, S.C.

To be published.

Macromolecule Content

Total Structure Weight: 616.11 kDa
Atom Count: 46,314
Modeled Residue Count: 4,995
Deposited Residue Count: 5,244
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
BH0493 protein	A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L	437	Halalkalibacterium halodurans C-125	Mutation(s): 0 Gene Names: BH0493
UniProt
Find proteins for Q9KFI6 (Halalkalibacterium halodurans (strain ATCC BAA-125 / DSM 18197 / FERM 7344 / JCM 9153 / C-125)) Explore Q9KFI6 Go to UniProtKB: Q9KFI6
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9KFI6
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ZN Query on ZN Download Ideal Coordinates CCD File SDF format, chain Z [auth E] SDF format, chain X [auth D] SDF format, chain T [auth C] SDF format, chain RA [auth L] SDF format, chain R [auth B] SDF format, chain PA [auth K] SDF format, chain P [auth A] SDF format, chain NA [auth J] SDF format, chain JA [auth I] SDF format, chain HA [auth H] SDF format, chain FA [auth G] SDF format, chain BA [auth F] MOL2 format, chain Z [auth E] MOL2 format, chain X [auth D] MOL2 format, chain T [auth C] MOL2 format, chain RA [auth L] MOL2 format, chain R [auth B] MOL2 format, chain PA [auth K] MOL2 format, chain P [auth A] MOL2 format, chain NA [auth J] MOL2 format, chain JA [auth I] MOL2 format, chain HA [auth H] MOL2 format, chain FA [auth G] MOL2 format, chain BA [auth F] mmCIF format, chain Z [auth E] mmCIF format, chain X [auth D] mmCIF format, chain T [auth C] mmCIF format, chain RA [auth L] mmCIF format, chain R [auth B] mmCIF format, chain PA [auth K] mmCIF format, chain P [auth A] mmCIF format, chain NA [auth J] mmCIF format, chain JA [auth I] mmCIF format, chain HA [auth H] mmCIF format, chain FA [auth G] mmCIF format, chain BA [auth F]	BA [auth F] FA [auth G] HA [auth H] JA [auth I] NA [auth J] BA [auth F], FA [auth G], HA [auth H], JA [auth I], NA [auth J], P [auth A], PA [auth K], R [auth B], RA [auth L], T [auth C], X [auth D], Z [auth E]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain BA [auth F] Focus chain FA [auth G] Focus chain HA [auth H] Focus chain JA [auth I] Focus chain NA [auth J] Focus chain P [auth A] Focus chain PA [auth K] Focus chain R [auth B] Focus chain RA [auth L] Focus chain T [auth C] Focus chain X [auth D] Focus chain Z [auth E] Interactions & Density Focus chain BA [auth F] Focus chain FA [auth G] Focus chain HA [auth H] Focus chain JA [auth I] Focus chain NA [auth J] Focus chain P [auth A] Focus chain PA [auth K] Focus chain R [auth B] Focus chain RA [auth L] Focus chain T [auth C] Focus chain X [auth D] Focus chain Z [auth E]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain Y [auth E] SDF format, chain V [auth D] SDF format, chain U [auth D] SDF format, chain S [auth C] SDF format, chain QA [auth L] SDF format, chain Q [auth B] SDF format, chain OA [auth K] SDF format, chain N [auth A] SDF format, chain M [auth A] SDF format, chain LA [auth J] SDF format, chain KA [auth J] SDF format, chain IA [auth I] SDF format, chain GA [auth H] SDF format, chain DA [auth G] SDF format, chain CA [auth G] SDF format, chain AA [auth F] MOL2 format, chain Y [auth E] MOL2 format, chain V [auth D] MOL2 format, chain U [auth D] MOL2 format, chain S [auth C] MOL2 format, chain QA [auth L] MOL2 format, chain Q [auth B] MOL2 format, chain OA [auth K] MOL2 format, chain N [auth A] MOL2 format, chain M [auth A] MOL2 format, chain LA [auth J] MOL2 format, chain KA [auth J] MOL2 format, chain IA [auth I] MOL2 format, chain GA [auth H] MOL2 format, chain DA [auth G] MOL2 format, chain CA [auth G] MOL2 format, chain AA [auth F] mmCIF format, chain Y [auth E] mmCIF format, chain V [auth D] mmCIF format, chain U [auth D] mmCIF format, chain S [auth C] mmCIF format, chain QA [auth L] mmCIF format, chain Q [auth B] mmCIF format, chain OA [auth K] mmCIF format, chain N [auth A] mmCIF format, chain M [auth A] mmCIF format, chain LA [auth J] mmCIF format, chain KA [auth J] mmCIF format, chain IA [auth I] mmCIF format, chain GA [auth H] mmCIF format, chain DA [auth G] mmCIF format, chain CA [auth G] mmCIF format, chain AA [auth F]	AA [auth F] CA [auth G] DA [auth G] GA [auth H] IA [auth I] AA [auth F], CA [auth G], DA [auth G], GA [auth H], IA [auth I], KA [auth J], LA [auth J], M [auth A], N [auth A], OA [auth K], Q [auth B], QA [auth L], S [auth C], U [auth D], V [auth D], Y [auth E]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain AA [auth F] Focus chain CA [auth G] Focus chain DA [auth G] Focus chain GA [auth H] Focus chain IA [auth I] Focus chain KA [auth J] Focus chain LA [auth J] Focus chain M [auth A] Focus chain N [auth A] Focus chain OA [auth K] Focus chain Q [auth B] Focus chain QA [auth L] Focus chain S [auth C] Focus chain U [auth D] Focus chain V [auth D] Focus chain Y [auth E] Interactions & Density Focus chain AA [auth F] Focus chain CA [auth G] Focus chain DA [auth G] Focus chain GA [auth H] Focus chain IA [auth I] Focus chain KA [auth J] Focus chain LA [auth J] Focus chain M [auth A] Focus chain N [auth A] Focus chain OA [auth K] Focus chain Q [auth B] Focus chain QA [auth L] Focus chain S [auth C] Focus chain U [auth D] Focus chain V [auth D] Focus chain Y [auth E]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain W [auth D] SDF format, chain O [auth A] SDF format, chain MA [auth J] SDF format, chain EA [auth G] MOL2 format, chain W [auth D] MOL2 format, chain O [auth A] MOL2 format, chain MA [auth J] MOL2 format, chain EA [auth G] mmCIF format, chain W [auth D] mmCIF format, chain O [auth A] mmCIF format, chain MA [auth J] mmCIF format, chain EA [auth G]	EA [auth G], MA [auth J], O [auth A], W [auth D]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain EA [auth G] Focus chain MA [auth J] Focus chain O [auth A] Focus chain W [auth D] Interactions & Density Focus chain EA [auth G] Focus chain MA [auth J] Focus chain O [auth A] Focus chain W [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.65 Å
R-Value Free: 0.224 (Depositor), 0.223 (DCC)
R-Value Work: 0.187 (Depositor), 0.187 (DCC)
R-Value Observed: 0.189 (Depositor)

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 121.995	α = 78.85
b = 122.208	β = 78.95
c = 127.582	γ = 80.92

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data collection
HKL-2000	data reduction
PHASER	phasing

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2007-07-24

Deposition Author(s):

New York SGX Research Center for Structural Genomics (NYSGXRC)

Revision History (Full details and data files)

Version 1.0: 2007-07-24
Type: Initial release
Version 1.1: 2008-05-01
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Version format compliance
Version 1.3: 2017-10-18
Changes: Refinement description
Version 1.4: 2018-11-14
Changes: Data collection, Structure summary
Version 1.5: 2021-02-03
Changes: Database references, Derived calculations, Structure summary
Version 1.6: 2023-08-30
Changes: Data collection, Database references, Refinement description