1V1Q | pdb_00001v1q

Crystal structure of PriB- a primosomal DNA replication protein of Escherichia coli

• PDB DOI: https://doi.org/10.2210/pdb1V1Q/pdb

• Classification: DNA BINDING
• Organism(s): Escherichia coli K-12
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2004-04-22 Released: 2004-10-25 
• Deposition Author(s): Liu, J.-H., Chang, T.-W., Huang, C.-Y., Chang, M.-C., Chen, S.-U., Wu, H.-N., Hsiao, C.-D.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 
  0.263 (Depositor), 0.257 (DCC) 
• R-Value Work: 
  0.206 (Depositor), 0.202 (DCC) 
• R-Value Observed: 
  0.206 (Depositor) 

Literature

Crystal Structure of Prib- a Primosomal DNA Replication Protein of Escherichia Coli

Liu, J.-H., Chang, T.-W., Huang, C.-Y., Chen, S.-U., Wu, H.-N., Chang, M.-C., Hsiao, C.-D.

(2004) J Biological Chem 279: 50465

• PubMed: 15383524 
• DOI: https://doi.org/10.1074/jbc.M406773200
• Primary Citation Related Structures: 
  1V1Q


• PubMed Abstract: 
  

  PriB is one of the Escherichia coli varphiX-type primosome proteins that are required for assembly of the primosome, a mobile multi-enzyme complex responsible for the initiation of DNA replication. Here we report the crystal structure of the E. coli PriB at 2.1 A resolution by multi-wavelength anomalous diffraction using a mercury derivative. The polypeptide chain of PriB is structurally similar to that of single-stranded DNA-binding protein (SSB). However, the biological unit of PriB is a dimer, not a homotetramer like SSB. Electrophoretic mobility shift assays demonstrated that PriB binds single-stranded DNA and single-stranded RNA with comparable affinity. We also show that PriB binds single-stranded DNA with certain base preferences. Based on the PriB structural information and biochemical studies, we propose that the potential tetramer formation surface and several other regions of PriB may participate in protein-protein interaction during DNA replication. These findings may illuminate the role of PriB in varphiX-type primosome assembly.

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Organizational Affiliation: 
• Graduate Institute of Life Sciences, National Defense Medical Center, Taipei, Taiwan 114.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PQS (software)

Macromolecule Content 

• Total Structure Weight: 29.95 kDa 
• Atom Count: 1,859 
• Modeled Residue Count: 223 
• Deposited Residue Count: 268 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PRIMOSOMAL REPLICATION PROTEIN N	A, B	134	Escherichia coli K-12	Mutation(s): 1
UniProt
Find proteins for P07013 (Escherichia coli (strain K12)) Explore P07013  Go to UniProtKB:  P07013

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CYS	C [auth A], D [auth A], E [auth B]	CYSTEINE C3 H7 N O2 S XUJNEKJLAYXESH-REOHCLBHSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free:  0.263 (Depositor), 0.257 (DCC) 
• R-Value Work:  0.206 (Depositor), 0.202 (DCC) 
• R-Value Observed: 0.206 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 39.322	α = 90
b = 57.358	β = 90
c = 97.019	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
DENZO	data reduction
SCALEPACK	data scaling
SOLVE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2004-10-25 
Deposition Author(s): Liu, J.-H., Chang, T.-W., Huang, C.-Y., Chang, M.-C., Chen, S.-U., Wu, H.-N., Hsiao, C.-D.

Revision History  

• Version 1.0: 2004-10-25
  Type: Initial release
  
• Version 1.1: 2011-05-08
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2023-11-08
  Changes: Data collection, Database references, Derived calculations, Other
• Version 1.4: 2024-11-20
  Changes: Structure summary