Download MendeleyCrystal structure of glycerophosphoryl diester phosphodiesterase (YP_677622.1) from Cytophaga hutchinsonii ATCC 33406 at 1.50 A resolution
Joint Center for Structural Genomics (JCSG)To be published.
3CH0
Crystal structure of glycerophosphoryl diester phosphodiesterase (YP_677622.1) from Cytophaga hutchinsonii ATCC 33406 at 1.50 A resolution
- PDB DOI: https://doi.org/10.2210/pdb3CH0/pdb
- Classification: HYDROLASE
- Organism(s): Cytophaga hutchinsonii ATCC 33406
- Expression System: Escherichia coli
- Mutation(s): No
- Deposited: 2008-03-06 Released: 2008-03-18
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 1.50 Å
- R-Value Free: 0.189
- R-Value Work: 0.158
- R-Value Observed: 0.160
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 |
| Glycerophosphodiester phosphodiesterase | A | 272 | Cytophaga hutchinsonii ATCC 33406 | Mutation(s): 0 Gene Names: YP_677622.1, ugpQ, CHU_1005 EC: 3.1.4.46 |  |
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
Protein Feature ViewExpand | |||||
| |||||
Small Molecules
| Ligands 3 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| CIT Query on CIT | B [auth A] | CITRIC ACID C6 H8 O7 KRKNYBCHXYNGOX-UHFFFAOYSA-N |  | Ligand Interaction | |
| GOL Query on GOL | S [auth A] | GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N |  | Ligand Interaction | |
| EDO Query on EDO | C [auth A], D [auth A], E [auth A], F [auth A], G [auth A], | 1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N |  | Ligand Interaction | |
| 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: 0.189
- R-Value Work: 0.158
- R-Value Observed: 0.160
- Space Group: P 21 21 21
- Diffraction Data: https://doi.org/10.18430/M33CH0
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 49.532 | α = 90 |
| b = 61.211 | β = 90 |
| c = 113.699 | γ = 90 |
| Software Name | Purpose |
|---|---|
| REFMAC | refinement |
| PHENIX | refinement |
| SOLVE | phasing |
| MolProbity | model building |
| SCALA | data scaling |
| PDB_EXTRACT | data extraction |
| MAR345 | data collection |
| MOSFLM | data reduction |
Entry History
Deposition Data
- Released Date: 2008-03-18 Deposition Author(s): Joint Center for Structural Genomics (JCSG)
Revision History (Full details and data files)
- Version 1.0: 2008-03-18
Type: Initial release - Version 1.1: 2011-07-13
Changes: Non-polymer description, 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
