Download MendeleyCrystal structure of Unknown protein from 2D-page (Spot PR51) (b2898) from Escherichia coli k12 at 1.30 A resolution
Joint Center for Structural Genomics (JCSG)To be published.
1VLY
Crystal structure of a putative aminomethyltransferase (ygfz) from escherichia coli at 1.30 A resolution
- PDB DOI: https://doi.org/10.2210/pdb1VLY/pdb
- Classification: TRANSFERASE
- Organism(s): Escherichia coli
- Expression System: Escherichia coli
- Mutation(s): Yes
- Deposited: 2004-08-20 Released: 2004-08-31
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 1.30 Å
- R-Value Free: 0.168
- R-Value Work: 0.134
- R-Value Observed: 0.136
wwPDB Validation 3D Report Full Report
This is version 1.3 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 |
| Unknown protein from 2D-page | 338 | Escherichia coli | Mutation(s): 9 Gene Names: ygfZ, b2898 |  | |
UniProt | |||||
Find proteins for P0ADE8 (Escherichia coli (strain K12)) Explore P0ADE8 Go to UniProtKB: P0ADE8 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | P0ADE8 | ||||
Sequence AnnotationsExpand | |||||
| |||||
Small Molecules
| Ligands 4 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| EDO Query on EDO | E [auth A], F [auth A], G [auth A] | 1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N |  | ||
| ACT Query on ACT | B [auth A] | ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M |  | ||
| CA Query on CA | C [auth A] | CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N |  | ||
| CL Query on CL | 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: 1.30 Å
- R-Value Free: 0.168
- R-Value Work: 0.134
- R-Value Observed: 0.136
- Space Group: P 1
- Diffraction Data: https://doi.org/10.18430/M31VLY
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 44.814 | α = 94.68 |
| b = 50.08 | β = 115.29 |
| c = 52.014 | γ = 116.46 |
| Software Name | Purpose |
|---|---|
| MOSFLM | data reduction |
| SCALA | data scaling |
| SHARP | phasing |
| REFMAC | refinement |
| CCP4 | data scaling |
Entry History
Deposition Data
- Released Date: 2004-08-31 Deposition Author(s): Joint Center for Structural Genomics (JCSG)
Revision History (Full details and data files)
- Version 1.0: 2004-08-31
Type: Initial release - Version 1.1: 2008-04-26
Changes: Version format compliance - Version 1.2: 2011-07-13
Changes: Version format compliance - Version 1.3: 2023-01-25
Changes: Database references, Derived calculations
