2Q08 | pdb_00002q08

Crystal structure of the protein BH0493 from Bacillus halodurans C-125 complexed with ZN

PDB DOI: https://doi.org/10.2210/pdb2Q08/pdb

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

Deposited: 2007-05-21 Released: 2007-06-19
Deposition Author(s): Fedorov, A.A., Fedorov, E.V., Patskovsky, Y., Sauder, J.M., Burley, S.K., Raushel, F., Almo, S.C., New York SGX Research Center for Structural Genomics (NYSGXRC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free:
0.239 (Depositor), 0.239 (DCC)
R-Value Work:
0.226 (Depositor), 0.226 (DCC)
R-Value Observed:
0.226 (Depositor)

wwPDB Validation 3D Report Full Report

This is version 1.5 of the entry. See complete history.

Literature

Crystal structure of Glucoronate Isomerase from Bacillus halodurans.

Fedorov, A.A., Fedorov, E.V., Patskovsky, Y., Sauder, J.M., Burley, S.K., Raushel, F.M., Almo, S.C.

To be published.

Macromolecule Content

Total Structure Weight: 601.13 kDa
Atom Count: 41,791
Modeled Residue Count: 4,956
Deposited Residue Count: 5,124
Unique protein chains: 1

Macromolecules

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| 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	427	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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9KFI6
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 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 J] SDF format, chain Y [auth J] SDF format, chain X [auth I] SDF format, chain W [auth H] SDF format, chain V [auth H] SDF format, chain U [auth G] SDF format, chain T [auth F] SDF format, chain S [auth E] SDF format, chain R [auth D] SDF format, chain Q [auth D] SDF format, chain P [auth C] SDF format, chain O [auth B] SDF format, chain N [auth A] SDF format, chain M [auth A] SDF format, chain BA [auth L] SDF format, chain AA [auth K] MOL2 format, chain Z [auth J] MOL2 format, chain Y [auth J] MOL2 format, chain X [auth I] MOL2 format, chain W [auth H] MOL2 format, chain V [auth H] MOL2 format, chain U [auth G] MOL2 format, chain T [auth F] MOL2 format, chain S [auth E] MOL2 format, chain R [auth D] MOL2 format, chain Q [auth D] MOL2 format, chain P [auth C] MOL2 format, chain O [auth B] MOL2 format, chain N [auth A] MOL2 format, chain M [auth A] MOL2 format, chain BA [auth L] MOL2 format, chain AA [auth K] mmCIF format, chain Z [auth J] mmCIF format, chain Y [auth J] mmCIF format, chain X [auth I] mmCIF format, chain W [auth H] mmCIF format, chain V [auth H] mmCIF format, chain U [auth G] mmCIF format, chain T [auth F] mmCIF format, chain S [auth E] mmCIF format, chain R [auth D] mmCIF format, chain Q [auth D] mmCIF format, chain P [auth C] mmCIF format, chain O [auth B] mmCIF format, chain N [auth A] mmCIF format, chain M [auth A] mmCIF format, chain BA [auth L] mmCIF format, chain AA [auth K]	AA [auth K] BA [auth L] M [auth A] N [auth A] O [auth B] AA [auth K], BA [auth L], M [auth A], N [auth A], O [auth B], P [auth C], Q [auth D], R [auth D], S [auth E], T [auth F], U [auth G], V [auth H], W [auth H], X [auth I], Y [auth J], Z [auth J]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain AA [auth K] Focus chain BA [auth L] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth B] Focus chain P [auth C] Focus chain Q [auth D] Focus chain R [auth D] Focus chain S [auth E] Focus chain T [auth F] Focus chain U [auth G] Focus chain V [auth H] Focus chain W [auth H] Focus chain X [auth I] Focus chain Y [auth J] Focus chain Z [auth J] Interactions & Density Focus chain AA [auth K] Focus chain BA [auth L] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth B] Focus chain P [auth C] Focus chain Q [auth D] Focus chain R [auth D] Focus chain S [auth E] Focus chain T [auth F] Focus chain U [auth G] Focus chain V [auth H] Focus chain W [auth H] Focus chain X [auth I] Focus chain Y [auth J] Focus chain Z [auth J]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.239 (Depositor), 0.239 (DCC)
R-Value Work: 0.226 (Depositor), 0.226 (DCC)
R-Value Observed: 0.226 (Depositor)

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 121.274	α = 78.82
b = 120.967	β = 78.67
c = 126.241	γ = 80.42

Software Package:

Software Name	Purpose
CNS	refinement
ADSC	data collection
DENZO	data reduction
SCALEPACK	data scaling
SHELX	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2007-06-19

Deposition Author(s):

New York SGX Research Center for Structural Genomics (NYSGXRC)

Revision History (Full details and data files)

Version 1.0: 2007-06-19
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: 2018-11-14
Changes: Data collection, Structure summary
Version 1.4: 2021-02-03
Changes: Database references, Derived calculations, Structure summary
Version 1.5: 2024-02-21
Changes: Data collection, Database references