Download MendeleyCrystal structure of putative hydrolase (YP_751971.1) from Shewanella frigidimarina NCIMB 400 at 1.80 A resolution
Joint Center for Structural Genomics (JCSG)To be published.
3LHO | pdb_00003lho
Crystal structure of putative hydrolase (YP_751971.1) from Shewanella frigidimarina NCIMB 400 at 1.80 A resolution
- PDB DOI: https://doi.org/10.2210/pdb3LHO/pdb
- Classification: HYDROLASE
- Organism(s): Shewanella frigidimarina NCIMB 400
- Expression System: Escherichia coli
- Mutation(s): No
- Deposited: 2010-01-22 Released: 2010-03-09
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 1.80 Å
- R-Value Free: 0.207 (Depositor), 0.220 (DCC)
- R-Value Work: 0.173 (Depositor), 0.180 (DCC)
- R-Value Observed: 0.175 (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 hydrolase | 267 | Shewanella frigidimarina NCIMB 400 | Mutation(s): 0 Gene Names: Sfri_3296 EC: 1.13.11.93 |  | |
UniProt | |||||
Find proteins for Q07XY2 (Shewanella frigidimarina (strain NCIMB 400)) Explore Q07XY2 Go to UniProtKB: Q07XY2 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | Q07XY2 | ||||
Sequence AnnotationsExpand | |||||
| |||||
Small Molecules
| Ligands 5 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| PG4 Query on PG4 | L [auth A] | TETRAETHYLENE GLYCOL C8 H18 O5 UWHCKJMYHZGTIT-UHFFFAOYSA-N |  | ||
| PEG Query on PEG | J [auth A], K [auth A] | DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N |  | ||
| SO4 Query on SO4 | C [auth A], D [auth A], E [auth A] | SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L |  | ||
| GOL Query on GOL | F [auth A], G [auth A], H [auth A], I [auth A] | GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N |  | ||
| NI Query on NI | B [auth A] | NICKEL (II) ION Ni VEQPNABPJHWNSG-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: 1.80 Å
- R-Value Free: 0.207 (Depositor), 0.220 (DCC)
- R-Value Work: 0.173 (Depositor), 0.180 (DCC)
- R-Value Observed: 0.175 (Depositor)
Diffraction Data: https://doi.org/10.18430/M33LHO
Space Group: P 21 21 21
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 42.098 | α = 90 |
| b = 75.035 | β = 90 |
| c = 91.112 | γ = 90 |
| Software Name | Purpose |
|---|---|
| REFMAC | refinement |
| PHENIX | refinement |
| SHELX | phasing |
| MolProbity | model building |
| XSCALE | data scaling |
| PDB_EXTRACT | data extraction |
| XDS | data reduction |
| SHELXD | phasing |
| autoSHARP | phasing |
Entry History
Deposition Data
- Released Date: 2010-03-09 Deposition Author(s): Joint Center for Structural Genomics (JCSG)
Revision History (Full details and data files)
- Version 1.0: 2010-03-09
Type: Initial release - Version 1.1: 2011-07-13
Changes: Advisory, Version format compliance - Version 1.2: 2017-11-01
Changes: 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
