Download MendeleyCrystal 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.
2Q04 | pdb_00002q04
2Q04 | pdb_00002q04
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 artemiae 255-15
- Expression System: Escherichia coli
- Mutation(s): Yes
- Deposited: 2007-05-18 Released: 2007-06-12
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 2.33 Å
- R-Value Free: 0.260 (Depositor), 0.290 (DCC)
- R-Value Work: 0.229 (Depositor)
- R-Value Observed: 0.231 (Depositor)
wwPDB Validation 3D Report Full Report
This is version 1.7 of the entry. See complete history.
Literature
To be published.
Macromolecule Content
- Total Structure Weight: 148.13 kDa
- Atom Count: 10,133
- Modeled Residue Count: 1,250
- Deposited Residue Count: 1,266
- Unique protein chains: 1
Macromolecules
Find similar proteins by:
| 3D Structure
Entity ID: 1 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| Acetoin utilization protein | 211 | Exiguobacterium artemiae 255-15 | Mutation(s): 8 Gene Names: ZP_00540088.1, ExigDRAFT_0571 |  | |
UniProt | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | B1YKD7 | ||||
Sequence AnnotationsExpand | |||||
Reference Sequence | |||||
Small Molecules
| Ligands 3 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| EDO Download:Ideal Coordinates CCD File | I [auth A] J [auth A] K [auth A] O [auth C] Q [auth D] | 1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N |  | ||
| ACY Download:Ideal Coordinates CCD File | L [auth A], T [auth E], U [auth E], X [auth F] | ACETIC ACID C2 H4 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-N |  | ||
| CA Download:Ideal Coordinates CCD File | G [auth A] H [auth A] M [auth B] N [auth C] P [auth D] | CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N |  | ||
| 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 (Depositor), 0.290 (DCC)
- R-Value Work: 0.229 (Depositor)
- R-Value Observed: 0.231 (Depositor)
Diffraction Data:
Space Group: P 1 21 1
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 70.87 | α = 90 |
| b = 128.58 | β = 108.43 |
| c = 108.43 | γ = 90 |
| 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 |
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 - Version 1.7: 2024-10-09
Changes: Data collection, Refinement description, Structure summary
