4AUW | pdb_00004auw

CRYSTAL STRUCTURE OF THE BZIP HOMODIMERIC MAFB IN COMPLEX WITH THE C- MARE BINDING SITE

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 
    0.290 (Depositor), 0.285 (DCC) 
  • R-Value Work: 
    0.255 (Depositor), 0.259 (DCC) 
  • R-Value Observed: 
    0.257 (Depositor) 

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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history. 

Literature

Expression, purification, crystallization and preliminary crystallographic analysis of the mouse transcription factor MafB in complex with its DNA-recognition motif Cmare

Textor, L.C., Wilmanns, M., Holton, S.J.

(2007) Acta Crystallogr Sect F Struct Biol Cryst Commun 63: 657-661

  • DOI: https://doi.org/10.1107/S1744309107031260
  • Primary Citation Related Structures: 
    4AUW

  • PubMed Abstract: 

    The MafB transcription factor (residues 211-305) has been overexpressed in and purified from Escherichia coli. A protein-DNA complex between the MafB homodimer and the 21 bp Maf-recognition sequence known as Cmare has been successfully reconstituted in vitro and subsequently crystallized. The diffraction properties of the protein-DNA complex crystals were improved using a combination of protein-construct boundary optimization and targeted mutagenesis to promote crystal lattice stability. Both native and mercury-derivatized crystals have been prepared using these optimized conditions. The crystals belong to space group P4(1)2(1)2 or P4(3)2(1)2, with unit-cell parameters a = b = 94.8, c = 197.9 A. An anomalous difference Patterson map computed using data collected from crystals grown in the presence of HgCl(2) reveals four peaks. This corresponds to two copies of the protein-DNA complex in the asymmetric unit, with a solvent content of 62% and a Matthews coefficient of 3.22 A(3) Da(-1).

    • Organizational Affiliation: 
    • EMBL DESY, Notkestrasse 85, D-22603 Hamburg, Germany.

Macromolecule Content 

  • Total Structure Weight: 72.88 kDa 
  • Atom Count: 4,665 
  • Modeled Residue Count: 439 
  • Deposited Residue Count: 468 
  • Unique protein chains: 1
  • Unique nucleic acid chains: 2

Macromolecules


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Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
TRANSCRIPTION FACTOR MAFB
A, B, E, F
96Mus musculusMutation(s): 1 
UniProt
Find proteins for P54841 (Mus musculus)
Explore P54841 
Go to UniProtKB:  P54841
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP54841
Sequence Annotations
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Reference Sequence
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Entity ID: 2
MoleculeChains LengthOrganismImage
C-MARE BINDING SITE (5'-D(*AP*TP*AP*AP*TP*GP*CP*TP* GP*AP*CP*GP*TP*CP*AP*GP*CP*AP*AP*TP*T)-3')
C, H
21synthetic construct
Sequence Annotations
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Reference Sequence
Find similar nucleic acids by:  Sequence
Entity ID: 3
MoleculeChains LengthOrganismImage
C-MARE BINDING SITE (5'-D(*AP*TP*AP*AP*TP*GP*CP*TP* GP*AP*CP*GP*TP*CP*AP*GP*CP*AP*AP*TP*T)-3')
D, G
21synthetic construct
Sequence Annotations
Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free:  0.290 (Depositor), 0.285 (DCC) 
  • R-Value Work:  0.255 (Depositor), 0.259 (DCC) 
  • R-Value Observed: 0.257 (Depositor) 
Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 94.964α = 90
b = 94.964β = 90
c = 200.111γ = 90
Software Package:
Software NamePurpose
REFMACrefinement

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-06-05
    Type: Initial release
  • Version 1.1: 2018-05-02
    Changes: Data collection, Database references
  • Version 1.2: 2024-05-08
    Changes: Data collection, Database references, Derived calculations, Other