Download MendeleyCrystal structure of putative peptidase (NP_348812.1) from CLOSTRIDIUM ACETOBUTYLICUM at 2.37 A resolution
Joint Center for Structural Genomics (JCSG)To be published.
3K9T | pdb_00003k9t
Crystal structure of putative peptidase (NP_348812.1) from CLOSTRIDIUM ACETOBUTYLICUM at 2.37 A resolution
- PDB DOI: https://doi.org/10.2210/pdb3K9T/pdb
- Classification: HYDROLASE
- Organism(s): Clostridium acetobutylicum
- Expression System: Escherichia coli
- Mutation(s): No
- Deposited: 2009-10-16 Released: 2009-11-10
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 2.37 Å
- R-Value Free: 0.212 (Depositor), 0.220 (DCC)
- R-Value Work: 0.169 (Depositor), 0.170 (DCC)
- R-Value Observed: 0.171 (Depositor)
wwPDB Validation 3D Report Full Report
This is version 1.5 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 |
| putative peptidase | 435 | Clostridium acetobutylicum | Mutation(s): 0 Gene Names: CA_C2195 |  | |
UniProt | |||||
Find proteins for Q97H19 (Clostridium acetobutylicum (strain ATCC 824 / DSM 792 / JCM 1419 / IAM 19013 / LMG 5710 / NBRC 13948 / NRRL B-527 / VKM B-1787 / 2291 / W)) Explore Q97H19 Go to UniProtKB: Q97H19 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | Q97H19 | ||||
Sequence AnnotationsExpand | |||||
| |||||
Small Molecules
| Ligands 4 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| MRD Query on MRD | F [auth A], G [auth A], H [auth A], I [auth A] | (4R)-2-METHYLPENTANE-2,4-DIOL C6 H14 O2 SVTBMSDMJJWYQN-RXMQYKEDSA-N |  | ||
| IMD Query on IMD | E [auth A] | IMIDAZOLE C3 H5 N2 RAXXELZNTBOGNW-UHFFFAOYSA-O |  | ||
| ZN Query on ZN | B [auth A] | ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N |  | ||
| CL Query on CL | C [auth A], D [auth A] | CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M |  | ||
| Modified Residues 1 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Type | Formula | 2D Diagram | Parent |
| MSE Query on MSE | A | L-PEPTIDE LINKING | C5 H11 N O2 Se |  | MET |
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 2.37 Å
- R-Value Free: 0.212 (Depositor), 0.220 (DCC)
- R-Value Work: 0.169 (Depositor), 0.170 (DCC)
- R-Value Observed: 0.171 (Depositor)
Diffraction Data: https://doi.org/10.18430/M33K9T
Space Group: H 3 2
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 153.782 | α = 90 |
| b = 153.782 | β = 90 |
| c = 168.378 | γ = 120 |
| Software Name | Purpose |
|---|---|
| REFMAC | refinement |
| PHENIX | refinement |
| SHELX | phasing |
| MolProbity | model building |
| SCALA | data scaling |
| PDB_EXTRACT | data extraction |
| MOSFLM | data reduction |
| SHELXD | phasing |
| autoSHARP | phasing |
Entry History
Deposition Data
- Released Date: 2009-11-10 Deposition Author(s): Joint Center for Structural Genomics (JCSG)
Revision History (Full details and data files)
- Version 1.0: 2009-11-10
Type: Initial release - Version 1.1: 2011-07-13
Changes: Advisory, Version format compliance - Version 1.2: 2017-10-25
Changes: Author supporting evidence, Refinement description - Version 1.3: 2019-07-17
Changes: Data collection, Derived calculations, Refinement description - Version 1.4: 2023-02-01
Changes: Database references, Derived calculations - Version 1.5: 2024-10-30
Changes: Data collection, Structure summary
