Download MendeleyCrystal structure of predicted HD superfamily hydrolase involved in NAD metabolism (NP_347894.1) from Clostridium acetobutylicum at 1.50 A resolution
Joint Center for Structural Genomics (JCSG)To be published.
3CCG | pdb_00003ccg
Crystal structure of predicted HD superfamily hydrolase involved in NAD metabolism (NP_347894.1) from Clostridium acetobutylicum at 1.50 A resolution
- PDB DOI: https://doi.org/10.2210/pdb3CCG/pdb
- Classification: HYDROLASE
- Organism(s): Clostridium acetobutylicum ATCC 824
- Expression System: Escherichia coli
- Mutation(s): No
- Deposited: 2008-02-25 Released: 2008-03-11
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 1.50 Å
- R-Value Free: 0.217 (Depositor), 0.220 (DCC)
- R-Value Work: 0.180 (Depositor), 0.190 (DCC)
- R-Value Observed: 0.182 (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 |
| HD superfamily hydrolase | 190 | Clostridium acetobutylicum ATCC 824 | Mutation(s): 0 Gene Names: NP_347894.1, CA_C1263 EC: 3.6.1.41 |  | |
UniProt | |||||
Find proteins for Q97JL1 (Clostridium acetobutylicum (strain ATCC 824 / DSM 792 / JCM 1419 / IAM 19013 / LMG 5710 / NBRC 13948 / NRRL B-527 / VKM B-1787 / 2291 / W)) Explore Q97JL1 Go to UniProtKB: Q97JL1 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | Q97JL1 | ||||
Sequence AnnotationsExpand | |||||
| |||||
Small Molecules
| Ligands 2 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| PO4 Query on PO4 | D [auth A] | PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K |  | ||
| FE Query on FE | B [auth A], C [auth A] | FE (III) ION Fe VTLYFUHAOXGGBS-UHFFFAOYSA-N |  | ||
| 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: 1.50 Å
- R-Value Free: 0.217 (Depositor), 0.220 (DCC)
- R-Value Work: 0.180 (Depositor), 0.190 (DCC)
- R-Value Observed: 0.182 (Depositor)
Diffraction Data: https://doi.org/10.18430/M33CCG
Space Group: C 1 2 1
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 90.54 | α = 90 |
| b = 36.32 | β = 125.46 |
| c = 72.6 | 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 |
| SHELXD | phasing |
| autoSHARP | phasing |
Entry History
Deposition Data
- Released Date: 2008-03-11 Deposition Author(s): Joint Center for Structural Genomics (JCSG)
Revision History (Full details and data files)
- Version 1.0: 2008-03-11
Type: Initial release - Version 1.1: 2011-07-13
Changes: Advisory, Version format compliance - Version 1.2: 2017-10-25
Changes: Refinement description - Version 1.3: 2019-07-24
Changes: Data collection, Derived calculations, Refinement description - Version 1.4: 2023-02-01
Changes: Database references, Derived calculations - Version 1.5: 2024-11-20
Changes: Data collection, Structure summary
