3K4H
CRYSTAL STRUCTURE OF putative transcriptional regulator LacI from Bacillus cereus subsp. cytotoxis NVH 391-98
- PDB DOI: https://doi.org/10.2210/pdb3K4H/pdb
- Classification: transcription regulator
- Organism(s): Bacillus cytotoxicus NVH 391-98
- Expression System: Escherichia coli BL21(DE3)
- Mutation(s): No
- Deposited: 2009-10-05 Released: 2009-11-10
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 2.80 Å
- R-Value Free: 0.244
- R-Value Work: 0.203
- R-Value Observed: 0.205
wwPDB Validation 3D Report Full Report
This is version 2.1 of the entry. See complete history.
Macromolecules
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 1 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| putative transcriptional regulator | 292 | Bacillus cytotoxicus NVH 391-98 | Mutation(s): 0 Gene Names: Bcer98_2711, Q2E7G6 |  | |
UniProt | |||||
Find proteins for D0VWZ8 (Bacillus cytotoxicus (strain DSM 22905 / CIP 110041 / 391-98 / NVH 391-98)) Explore D0VWZ8 Go to UniProtKB: D0VWZ8 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | D0VWZ8 | ||||
Sequence AnnotationsExpand | |||||
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Oligosaccharides
Small Molecules
| Modified Residues 1 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Type | Formula | 2D Diagram | Parent |
| MSE Query on MSE | A, B | L-PEPTIDE LINKING | C5 H11 N O2 Se |  | MET |
Biologically Interesting Molecules (External Reference) 1 Unique
Entity ID: 2 | |||||
|---|---|---|---|---|---|
| ID | Chains | Name | Type/Class | 2D Diagram | 3D Interactions |
| PRD_900001 Query on PRD_900001 | C, D | alpha-maltose | Oligosaccharide / Nutrient |  | |
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 2.80 Å
- R-Value Free: 0.244
- R-Value Work: 0.203
- R-Value Observed: 0.205
- Space Group: P 41 21 2
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 98.607 | α = 90 |
| b = 98.607 | β = 90 |
| c = 186.749 | γ = 90 |
| Software Name | Purpose |
|---|---|
| DENZO | data reduction |
| SCALEPACK | data scaling |
| REFMAC | refinement |
| PDB_EXTRACT | data extraction |
| HKL-2000 | data reduction |
| SHELXS | phasing |
Entry History
Deposition Data
- Released Date: 2009-11-10 Deposition Author(s): Malashkevich, V.N., Toro, R., Morano, C., Sauder, J.M., Burley, S.K., Almo, S.C., New York SGX Research Center for Structural Genomics (NYSGXRC)
Revision History (Full details and data files)
- Version 1.0: 2009-11-10
Type: Initial release - Version 1.1: 2011-07-13
Changes: Advisory, Refinement description, Version format compliance - Version 1.2: 2012-10-24
Changes: Structure summary - Version 1.3: 2017-11-01
Changes: Refinement description - Version 1.4: 2018-11-21
Changes: Data collection, Structure summary - Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Atomic model, Data collection, Derived calculations, Non-polymer description, Structure summary - Version 2.1: 2021-02-10
Changes: Database references, Structure summary
