4MLZ

Crystal structure of periplasmic binding protein from Jonesia denitrificans


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.72 Å
  • R-Value Free: 0.193 
  • R-Value Work: 0.135 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Crystal structure of periplasmic binding protein from Jonesia denitrificans

Chang, C.Chhor, G.Endres, M.Joachimiak, A.

To be published.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Periplasmic binding protein
A, B
330Jonesia denitrificans (strain ATCC 14870 / DSM 20603 / CIP 55134)N/A
Find proteins for C7R301 (Jonesia denitrificans (strain ATCC 14870 / DSM 20603 / CIP 55134))
Go to UniProtKB:  C7R301
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
K
Query on K

Download SDF File 
Download CCD File 
A, B
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
 Ligand Interaction
CA
Query on CA

Download SDF File 
Download CCD File 
A, B
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A, B
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.72 Å
  • R-Value Free: 0.193 
  • R-Value Work: 0.135 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 59.678α = 90.00
b = 72.741β = 101.32
c = 71.306γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
MLPHAREphasing
HKL-3000data reduction
HKL-3000phasing
SBC-Collectdata collection
ARP/wARPmodel building
HKL-3000data scaling
DMphasing
RESOLVEphasing
PDB_EXTRACTdata extraction
Cootmodel building
SHELXDEphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-09-18
    Type: Initial release
  • Version 1.1: 2017-11-15
    Type: Refinement description