4I1D

The crystal structure of an ABC transporter substrate-binding protein from Bradyrhizobium japonicum USDA 110

Structural Biology Knowledgebase: 4I1D SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.209
  • R-Value Work: 0.172

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 4I1D

Classification: TRANSPORT PROTEIN

Total Structure Weight: 149248.39

Macromolecule Entities
Molecule Chains Length Organism Details
ABC transporter substrate-binding protein A, B, C, D 324 Bradyrhizobium diazoefficiens Gene Name(s): bll6825

Small Molecules
Ligands 4 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
MLT
Query on MLT

A, B, C, D D-MALATE
(2R)-2-HYDROXYBUTANEDIOIC ACID; 2-HYDROXY- SUCCINIC ACID (Synonym)
C4 H6 O5
BJEPYKJPYRNKOW-UWTATZPHSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
SO4
Query on SO4

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

A, B, C, D GLYCEROL
2, (Synonym)
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
ACT
Query on ACT

A, B, C, D ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
Modified Residues 1 Unique
ID Chains Type Formula 2D Diagram Parent
MSE
Query on MSE
A, B, C, D L-PEPTIDE LINKING C5 H11 N O2 Se MET

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.209
  • R-Value Work: 0.172
  • Space Group: P 32 2 1
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 136.64 α = 90.00
b = 136.64 β = 90.00
c = 185.63 γ = 120.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2012-11-20
  • Released Date: 2012-12-05
  • Deposition author(s): Fan, Y., Tan, K., Mack, J., Zerbs, S., Collart, F., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Revision History

  • 2013-09-25
    Type: Citation | Details: Citation update
  • 2013-05-15
    Type: Citation | Details: Citation update