Download MendeleySubstrate recognition mechanism of NRPS adenylation protein from Streptomyces
Ueki, M., Okumura, H., Osada, H.To be published.
3VNS
Co-crystal structure of NRPS adenylation protein CytC1 with D-valine and AMP from streptomyces
- PDB DOI: https://doi.org/10.2210/pdb3VNS/pdb
- Classification: LIGASE
- Organism(s): Streptomyces sp.
- Expression System: Escherichia coli
- Mutation(s): No
- Deposited: 2012-01-17 Released: 2013-01-23
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 2.00 Å
- R-Value Free: 0.216
- R-Value Work: 0.191
- R-Value Observed: 0.193
Starting Model: experimental
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This is version 1.2 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 |
| NRPS adenylation protein CytC1 | 544 | Streptomyces sp. | Mutation(s): 0 |  | |
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
Sequence AnnotationsExpand | |||||
| |||||
Small Molecules
| Ligands 2 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| AMP Query on AMP | B [auth A] | ADENOSINE MONOPHOSPHATE C10 H14 N5 O7 P UDMBCSSLTHHNCD-KQYNXXCUSA-N |  | ||
| DVA Query on DVA | C [auth A] | D-VALINE C5 H11 N O2 KZSNJWFQEVHDMF-SCSAIBSYSA-N |  | ||
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 2.00 Å
- R-Value Free: 0.216
- R-Value Work: 0.191
- R-Value Observed: 0.193
- Space Group: I 2 3
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 156.544 | α = 90 |
| b = 156.544 | β = 90 |
| c = 156.544 | γ = 90 |
| Software Name | Purpose |
|---|---|
| DENZO | data reduction |
| SCALEPACK | data scaling |
| MOLREP | phasing |
| PHENIX | refinement |
| PDB_EXTRACT | data extraction |
| BSS | data collection |
| HKL-2000 | data reduction |
| HKL-2000 | data scaling |
Entry History
Deposition Data
- Released Date: 2013-01-23 Deposition Author(s): Okumura, H., Ueki, M., Shiro, Y., Osada, H.
Revision History (Full details and data files)
- Version 1.0: 2013-01-23
Type: Initial release - Version 1.1: 2017-11-22
Changes: Refinement description - Version 1.2: 2023-11-08
Changes: Data collection, Database references, Derived calculations, Refinement description
