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- PDB-1woc: Crystal structure of PriB -

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Basic information

Entry
Database: PDB / ID: 1woc
TitleCrystal structure of PriB
ComponentsPrimosomal replication protein n
KeywordsDNA BINDING PROTEIN / Oligonucleotide Binding fold
Function / homology
Function and homology information


pre-primosome complex / DnaB-DnaC-DnaT-PriA-PriB complex / plasmid maintenance / primosome complex / DNA replication, synthesis of primer / replication fork processing / DNA unwinding involved in DNA replication / DNA replication initiation / response to radiation / single-stranded DNA binding / identical protein binding
Similarity search - Function
Primosomal replication protein PriB / Single-strand binding protein family / Single-strand binding (SSB) domain profile. / Primosome PriB/single-strand DNA-binding / Nucleic acid-binding proteins / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Nucleic acid-binding, OB-fold / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Primosomal replication protein N
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2 Å
AuthorsShioi, S. / Ose, T. / Maenaka, K. / Abe, Y. / Kohda, D. / Katayama, T. / Ueda, T.
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2005
Title: Crystal structure of a biologically functional form of PriB from Escherichia coli reveals a potential single-stranded DNA-binding site
Authors: Shioi, S. / Ose, T. / Maenaka, K. / Shiroishi, M. / Abe, Y. / Kohda, D. / Katayama, T. / Ueda, T.
History
DepositionAug 13, 2004Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 25, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Dec 5, 2012Group: Derived calculations

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Primosomal replication protein n
B: Primosomal replication protein n
C: Primosomal replication protein n
D: Primosomal replication protein n


Theoretical massNumber of molelcules
Total (without water)45,6874
Polymers45,6874
Non-polymers00
Water3,639202
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Primosomal replication protein n
D: Primosomal replication protein n


Theoretical massNumber of molelcules
Total (without water)22,8442
Polymers22,8442
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2700 Å2
ΔGint-16 kcal/mol
Surface area10780 Å2
MethodPISA
3
B: Primosomal replication protein n

C: Primosomal replication protein n


Theoretical massNumber of molelcules
Total (without water)22,8442
Polymers22,8442
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_456-x-1/2,y+1/2,-z+11
Buried area2610 Å2
ΔGint-20 kcal/mol
Surface area10760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)103.521, 70.317, 74.805
Angle α, β, γ (deg.)90.00, 131.59, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
Primosomal replication protein n / Primosomal protein B / PriB


Mass: 11421.789 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Plasmid: pET22b(+) / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P07013
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 202 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.18 Å3/Da / Density % sol: 43.07 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 25%(v/v) MPD, 50mM Magnesium Chloride, 100mM Tris-HCl, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL38B1 / Wavelength: 0.97137, 0.9790, 0.9792
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 16, 2004
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.971371
20.9791
30.97921
ReflectionResolution: 2→50 Å / Num. obs: 27253 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.8 % / Biso Wilson estimate: 36.12 Å2 / Rmerge(I) obs: 0.062 / Net I/σ(I): 22.6
Reflection shellResolution: 2→2.07 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.112 / Num. unique all: 2719 / % possible all: 99.9

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Processing

Software
NameClassification
HKL-2000data collection
SCALEPACKdata scaling
SOLVEphasing
CNSrefinement
HKL-2000data reduction
RefinementMethod to determine structure: MAD / Resolution: 2→9 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber / Details: Used weighted full matrix least squares procedure.
RfactorNum. reflection% reflectionSelection details
Rfree0.2762 2631 -RANDOM
Rwork0.221 ---
all-26927 --
obs-26749 99.3 %-
Displacement parametersBiso mean: 28.3296 Å2
Baniso -1Baniso -2Baniso -3
1-5.766 Å20 Å21.713 Å2
2---10.898 Å20 Å2
3---5.132 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.32 Å0.26 Å
Luzzati d res low-5 Å
Luzzati sigma a0.26 Å0.21 Å
Refinement stepCycle: LAST / Resolution: 2→9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3068 0 0 202 3270
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008983
X-RAY DIFFRACTIONc_angle_deg1.52129
X-RAY DIFFRACTIONc_dihedral_angle_d27.34622
X-RAY DIFFRACTIONc_improper_angle_d0.88555
LS refinement shellResolution: 2→2.07 Å
RfactorNum. reflection% reflection
Rfree0.32712 266 -
Rwork0.2785 --
obs-2644 97.97 %

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