3MD9

Structure of apo form of a periplasmic heme binding protein

Structural Biology Knowledgebase: 3MD9 SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.5 Å
  • R-Value Free: 0.181
  • R-Value Work: 0.152

Literature

Macromolecules
Sequence Display for 3MD9

Classification: TRANSPORT PROTEIN

Total Structure Weight: 54682.14

Macromolecule Entities
Molecule Chains Length Organism Details
Hemin-binding periplasmic protein hmuT A, B 255 Yersinia pestis Gene Name(s): hmuT YPO0281 y0541 YP_0436
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

Small Molecules
Ligands 3 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
SO4
Query on SO4

B SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
GOL
Query on GOL

A GLYCEROL
2, (Synonym)
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
BR
Query on BR

A, B BROMIDE ION
Br
CPELXLSAUQHCOX-UHFFFAOYSA-M
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.5 Å
  • R-Value Free: 0.181
  • R-Value Work: 0.152
  • Space Group: P 1 21 1
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 61.71 α = 90.00
b = 66.74 β = 110.70
c = 62.27 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2010-03-30
  • Released Date: 2010-09-15
  • Deposition author(s): Mattle, D., Goetz, B.A., Locher, K.P.

Revision History

  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4