3IEH | pdb_00003ieh

Crystal structure of Putative metallopeptidase (YP_001051774.1) from SHEWANELLA BALTICA OS155 at 2.45 A resolution

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.45 Å
  • R-Value Free: 
    0.222 (Depositor), 0.219 (DCC) 
  • R-Value Work: 
    0.164 (Depositor), 0.171 (DCC) 
  • R-Value Observed: 
    0.167 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 3IEH

This is version 1.5 of the entry. See complete history. 

Literature

Crystal structure of Putative metallopeptidase (YP_001051774.1) from SHEWANELLA BALTICA OS155 at 2.45 A resolution

Joint Center for Structural Genomics (JCSG)

To be published.

Macromolecule Content 

  • Total Structure Weight: 31.82 kDa 
  • Atom Count: 2,207 
  • Modeled Residue Count: 268 
  • Deposited Residue Count: 276 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:
|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Putative metallopeptidase276Shewanella baltica OS155Mutation(s): 0 
Gene Names: Sbal_3428, YP_001051774.1
UniProt
Find proteins for A3D842 (Shewanella baltica (strain OS155 / ATCC BAA-1091))
Explore A3D842 
Go to UniProtKB:  A3D842
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA3D842
Sequence Annotations
Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PGE

Query on PGE


Download:Ideal Coordinates CCD File
M [auth A],
N [auth A]		TRIETHYLENE GLYCOL
C6 H14 O4
ZIBGPFATKBEMQZ-UHFFFAOYSA-N
PEG

Query on PEG


Download:Ideal Coordinates CCD File
J [auth A],
K [auth A],
L [auth A]		DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
GOL

Query on GOL


Download:Ideal Coordinates CCD File
D [auth A]
E [auth A]
F [auth A]
G [auth A]
H [auth A]
D [auth A],
E [auth A],
F [auth A],
G [auth A],
H [auth A],
I [auth A]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
ZN

Query on ZN


Download:Ideal Coordinates CCD File
B [auth A]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
UNL

Query on UNL


Download:Ideal Coordinates CCD File
C [auth A]Unknown ligand
PTFCDOFLOPIGGS-UHFFFAOYSA-N
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: 2.45 Å
  • R-Value Free:  0.222 (Depositor), 0.219 (DCC) 
  • R-Value Work:  0.164 (Depositor), 0.171 (DCC) 
  • R-Value Observed: 0.167 (Depositor) 
Space Group: P 65
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 80.958α = 90
b = 80.958β = 90
c = 87.94γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
PHENIXrefinement
SHELXphasing
MolProbitymodel building
SCALAdata scaling
PDB_EXTRACTdata extraction
MOSFLMdata reduction
SHARPphasing

Structure Validation

View Full Validation Report



View more in-depth experimental data

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2009-08-04
    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
  • Version 1.5: 2024-11-20
    Changes: Data collection, Structure summary