Download MendeleyThe crystal structure of a solute-binding protein from Anabaena variabilis ATCC 29413 in complex with pyruvic acid
Tan, K., Li, H., Jedrzejczak, R., Joachimiak, A.To be published.
4RV5
The crystal structure of a solute-binding protein from Anabaena variabilis ATCC 29413 in complex with pyruvic acid
- PDB DOI: https://doi.org/10.2210/pdb4RV5/pdb
- Classification: TRANSPORT PROTEIN
- Organism(s): Trichormus variabilis ATCC 29413
- Expression System: Escherichia coli BL21(DE3)
- Mutation(s): No
- Deposited: 2014-11-24 Released: 2014-12-10
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 1.04 Å
- R-Value Free: 0.131
- R-Value Work: 0.112
- R-Value Observed: 0.113
wwPDB Validation 3D Report Full Report
This is version 2.0 of the entry. See complete history.
Literature
To be published.
Macromolecules
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 1 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| Amino acid/amide ABC transporter substrate-binding protein, HAAT family | 395 | Trichormus variabilis ATCC 29413 | Mutation(s): 0 Gene Names: Ava_0465 |  | |
UniProt | |||||
Find proteins for Q3MFZ5 (Trichormus variabilis (strain ATCC 29413 / PCC 7937)) Explore Q3MFZ5 Go to UniProtKB: Q3MFZ5 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | Q3MFZ5 | ||||
Sequence AnnotationsExpand | |||||
| |||||
Small Molecules
| Ligands 3 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| PYR Query on PYR | C [auth A], F [auth B] | PYRUVIC ACID C3 H4 O3 LCTONWCANYUPML-UHFFFAOYSA-N |  | ||
| FMT Query on FMT | E [auth A] | FORMIC ACID C H2 O2 BDAGIHXWWSANSR-UHFFFAOYSA-N |  | ||
| MG Query on MG | D [auth A], G [auth B] | MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N |  | ||
| 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 |
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 1.04 Å
- R-Value Free: 0.131
- R-Value Work: 0.112
- R-Value Observed: 0.113
- Space Group: C 2 2 21
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 98.525 | α = 90 |
| b = 100.588 | β = 90 |
| c = 150.602 | γ = 90 |
| Software Name | Purpose |
|---|---|
| SBC-Collect | data collection |
| SHELXD | phasing |
| MLPHARE | phasing |
| DM | model building |
| DENZO | data reduction |
| SCALEPACK | data scaling |
| PHENIX | refinement |
| HKL-3000 | data reduction |
| HKL-3000 | data scaling |
| DM | phasing |
Entry History
Deposition Data
- Released Date: 2014-12-10 Deposition Author(s): Tan, K., Li, H., Jedrzejczak, R., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)
Revision History (Full details and data files)
- Version 1.0: 2014-12-10
Type: Initial release - Version 1.1: 2015-01-28
Changes: Structure summary - Version 1.2: 2017-11-22
Changes: Refinement description - Version 2.0: 2023-11-15
Changes: Atomic model, Data collection, Database references, Derived calculations
