2Q04

Crystal structure of acetoin utilization protein (ZP_00540088.1) from Exiguobacterium sibiricum 255-15 at 2.33 A resolution

PDB DOI: https://doi.org/10.2210/pdb2Q04/pdb

Classification: TRANSFERASE
Organism(s): Exiguobacterium sibiricum 255-15
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2007-05-18 Released: 2007-06-12
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.33 Å
R-Value Free: 0.260
R-Value Work: 0.229
R-Value Observed: 0.231

wwPDB Validation 3D Report Full Report

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

Literature

Crystal structure of acetoin utilization protein (ZP_00540088.1) from Exiguobacterium sibiricum 255-15 at 2.33 A resolution

Joint Center for Structural Genomics (JCSG)

To be published.

Macromolecule Content

Total Structure Weight: 148.13 kDa
Atom Count: 10,133
Modelled Residue Count: 1,250
Deposited Residue Count: 1,266
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Acetoin utilization protein	A, B, C, D, E A, B, C, D, E, F	211	Exiguobacterium sibiricum 255-15	Mutation(s): 8 Gene Names: ZP_00540088.1, ExigDRAFT_0571
UniProt
Find proteins for B1YKD7 (Exiguobacterium sibiricum (strain DSM 17290 / CIP 109462 / JCM 13490 / 255-15)) Explore B1YKD7 Go to UniProtKB: B1YKD7
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	B1YKD7
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
EDO Query on EDO 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 O [auth C] SDF format, chain Q [auth D] SDF format, chain R [auth D] SDF format, chain W [auth F] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain O [auth C] MOL2 format, chain Q [auth D] MOL2 format, chain R [auth D] MOL2 format, chain W [auth F]	I [auth A] J [auth A] K [auth A] O [auth C] Q [auth D] I [auth A], J [auth A], K [auth A], O [auth C], Q [auth D], R [auth D], W [auth F]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain O [auth C] Focus chain Q [auth D] Focus chain R [auth D] Focus chain W [auth F] Interactions & Density Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain O [auth C] Focus chain Q [auth D] Focus chain R [auth D] Focus chain W [auth F]
ACY Query on ACY Download Ideal Coordinates CCD File SDF format, chain L [auth A] SDF format, chain T [auth E] SDF format, chain U [auth E] SDF format, chain X [auth F] MOL2 format, chain L [auth A] MOL2 format, chain T [auth E] MOL2 format, chain U [auth E] MOL2 format, chain X [auth F]	L [auth A], T [auth E], U [auth E], X [auth F]	ACETIC ACID C₂ H₄ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-N		Interactions Focus chain L [auth A] Focus chain T [auth E] Focus chain U [auth E] Focus chain X [auth F] Interactions & Density Focus chain L [auth A] Focus chain T [auth E] Focus chain U [auth E] Focus chain X [auth F]
CA Query on CA Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain M [auth B] SDF format, chain N [auth C] SDF format, chain P [auth D] SDF format, chain S [auth E] SDF format, chain V [auth F] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain M [auth B] MOL2 format, chain N [auth C] MOL2 format, chain P [auth D] MOL2 format, chain S [auth E] MOL2 format, chain V [auth F]	G [auth A] H [auth A] M [auth B] N [auth C] P [auth D] G [auth A], H [auth A], M [auth B], N [auth C], P [auth D], S [auth E], V [auth F]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain H [auth A] Focus chain M [auth B] Focus chain N [auth C] Focus chain P [auth D] Focus chain S [auth E] Focus chain V [auth F] Interactions & Density Focus chain G [auth A] Focus chain H [auth A] Focus chain M [auth B] Focus chain N [auth C] Focus chain P [auth D] Focus chain S [auth E] Focus chain V [auth F]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE Query on MSE	A, B, C, D, E A, B, C, D, E, F	L-PEPTIDE LINKING	C₅ H₁₁ N O₂ Se		MET

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.33 Å
R-Value Free: 0.260
R-Value Work: 0.229
R-Value Observed: 0.231
Space Group: P 1 2₁ 1
Diffraction Data: https://doi.org/10.18430/M32Q04

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 70.87	α = 90
b = 128.58	β = 108.43
c = 108.43	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: 2007-06-12

Deposition Author(s):

Joint Center for Structural Genomics (JCSG)

Revision History (Full details and data files)

Version 1.0: 2007-06-12
Type: Initial release
Version 1.1: 2008-05-01
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Advisory, Source and taxonomy, Version format compliance
Version 1.3: 2017-10-18
Changes: Refinement description
Version 1.4: 2017-10-25
Changes: Author supporting evidence
Version 1.5: 2019-07-24
Changes: Data collection, Derived calculations, Refinement description
Version 1.6: 2023-01-25
Changes: Database references, Derived calculations

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Help and Resources

2Q04

Crystal structure of acetoin utilization protein (ZP_00540088.1) from Exiguobacterium sibiricum 255-15 at 2.33 A resolution

Crystal structure of acetoin utilization protein (ZP_00540088.1) from Exiguobacterium sibiricum 255-15 at 2.33 A resolution

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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Experimental Data

Structure Validation

Deposition Data

Revision History (Full details and data files)