1VLY | pdb_00001vly

Crystal structure of a putative aminomethyltransferase (ygfz) from escherichia coli at 1.30 A resolution


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.30 Å
  • R-Value Free: 
    0.168 (Depositor), 0.180 (DCC) 
  • R-Value Work: 
    0.134 (Depositor), 0.150 (DCC) 
  • R-Value Observed: 
    0.136 (Depositor) 

wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

Crystal 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.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Unknown protein from 2D-page338Escherichia coliMutation(s): 9 
Gene Names: ygfZb2898
UniProt
Find proteins for P0ADE8 (Escherichia coli (strain K12))
Explore P0ADE8 
Go to UniProtKB:  P0ADE8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0ADE8
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
EDO
Query on EDO

Download Ideal Coordinates CCD File 
E [auth A],
F [auth A],
G [auth A]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
ACT
Query on ACT

Download Ideal Coordinates CCD File 
B [auth A]ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
CA
Query on CA

Download Ideal Coordinates CCD File 
C [auth A]CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
CL
Query on CL

Download Ideal Coordinates CCD File 
D [auth A]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
MSE
Query on MSE
A
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.30 Å
  • R-Value Free:  0.168 (Depositor), 0.180 (DCC) 
  • R-Value Work:  0.134 (Depositor), 0.150 (DCC) 
  • R-Value Observed: 0.136 (Depositor) 
Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 44.814α = 94.68
b = 50.08β = 115.29
c = 52.014γ = 116.46
Software Package:
Software NamePurpose
MOSFLMdata reduction
SCALAdata scaling
SHARPphasing
REFMACrefinement
CCP4data scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

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
  • Version 1.4: 2024-10-09
    Changes: Data collection, Structure summary