Download MendeleyCrystal structure of ketosteroid isomerase-like protein (YP_049581.1) from ERWINIA CAROTOVORA ATROSEPTICA SCRI1043 at 2.40 A resolution
Joint Center for Structural Genomics (JCSG)To be published.
3D9R
Crystal structure of ketosteroid isomerase-like protein (YP_049581.1) from ERWINIA CAROTOVORA ATROSEPTICA SCRI1043 at 2.40 A resolution
- PDB DOI: https://doi.org/10.2210/pdb3D9R/pdb
- Classification: ISOMERASE
- Organism(s): Pectobacterium atrosepticum
- Expression System: Escherichia coli
- Mutation(s): No
- Deposited: 2008-05-27 Released: 2008-07-01
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 2.40 Å
- R-Value Free: 0.219
- R-Value Work: 0.182
- R-Value Observed: 0.184
wwPDB Validation 3D Report Full Report
This is version 1.4 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 |
| ketosteroid isomerase-like protein | 135 | Pectobacterium atrosepticum | Mutation(s): 0 Gene Names: YP_049581.1, ECA1476 |  | |
UniProt | |||||
Find proteins for Q6D750 (Pectobacterium atrosepticum (strain SCRI 1043 / ATCC BAA-672)) Explore Q6D750 Go to UniProtKB: Q6D750 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | Q6D750 | ||||
Sequence AnnotationsExpand | |||||
| |||||
Small Molecules
| Ligands 3 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| GOL Query on GOL | G [auth A], I [auth B], J [auth B], M [auth D] | GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N |  | ||
| NA Query on NA | E [auth A] | SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N |  | ||
| UNL Query on UNL | F [auth A], H [auth B], K [auth C], L [auth D] | Unknown ligand FKNQFGJONOIPTF-UHFFFAOYSA-N | |||
| Modified Residues 1 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Type | Formula | 2D Diagram | Parent |
| MSE Query on MSE | A, B, C, D | L-PEPTIDE LINKING | C5 H11 N O2 Se |  | MET |
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 2.40 Å
- R-Value Free: 0.219
- R-Value Work: 0.182
- R-Value Observed: 0.184
- Space Group: C 2 2 21
- Diffraction Data: https://doi.org/10.18430/M33D9R
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 115.998 | α = 90 |
| b = 135.416 | β = 90 |
| c = 139.164 | γ = 90 |
| Software Name | Purpose |
|---|---|
| REFMAC | refinement |
| PHENIX | refinement |
| SOLVE | phasing |
| MolProbity | model building |
| SCALA | data scaling |
| PDB_EXTRACT | data extraction |
| MOSFLM | data reduction |
Entry History
Deposition Data
- Released Date: 2008-07-01 Deposition Author(s): Joint Center for Structural Genomics (JCSG)
Revision History (Full details and data files)
- Version 1.0: 2008-07-01
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: 2019-07-24
Changes: Data collection, Derived calculations, Refinement description - Version 1.4: 2023-02-01
Changes: Database references, Derived calculations
