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- PDB-2ccz: Crystal structure of E. coli primosomol protein PriB bound to ssDNA -

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Basic information

Entry
Database: PDB / ID: 2ccz
TitleCrystal structure of E. coli primosomol protein PriB bound to ssDNA
Components
  • 5'-D(*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP *TP*TP*TP*TP*T)-3'
  • PRIMOSOMAL REPLICATION PROTEIN N
KeywordsDNA/REPLICATION / PRIMOSOME / PRIB / DNA REPLICATION / DNA REPAIR / DNA RECOMBINATION / SSDNA / SINGLE-STRANDED DNA / DNA-PROTEIN COMPLEX / DNA-REPLICATION complex
Function / homology
Function and homology information


pre-primosome complex / DnaB-DnaC-DnaT-PriA-PriB complex / primosome complex / plasmid maintenance / DNA replication, synthesis of primer / replication fork processing / DNA replication initiation / response to radiation / single-stranded DNA binding / DNA replication ...pre-primosome complex / DnaB-DnaC-DnaT-PriA-PriB complex / primosome complex / plasmid maintenance / DNA replication, synthesis of primer / replication fork processing / DNA replication initiation / response to radiation / single-stranded DNA binding / DNA replication / RNA binding / identical protein binding
Similarity search - Function
Primosomal replication protein PriB / Another single-strand binding protein family / 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
DNA / DNA (> 10) / Replication restart protein PriB
Similarity search - Component
Biological speciesESCHERICHIA COLI (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsHuang, C.-Y. / Hsu, C.-H. / Wu, H.-N. / Sun, Y.-J. / Hsiao, C.-D.
CitationJournal: Nucleic Acids Res. / Year: 2006
Title: Complexed Crystal Structure of Replication Restart Primsome Protein Prib Reveals a Novel Single-Stranded DNA-Binding Mode.
Authors: Huang, C.-Y. / Hsu, C.-H. / Sun, Y.-J. / Wu, H.-N. / Hsiao, C.-D.
History
DepositionJan 19, 2006Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 18, 2006Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf
Revision 1.4Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PRIMOSOMAL REPLICATION PROTEIN N
B: PRIMOSOMAL REPLICATION PROTEIN N
C: 5'-D(*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP *TP*TP*TP*TP*T)-3'


Theoretical massNumber of molelcules
Total (without water)31,8893
Polymers31,8893
Non-polymers00
Water2,144119
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)45.537, 51.148, 99.096
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein PRIMOSOMAL REPLICATION PROTEIN N / PRIB


Mass: 13685.733 Da / Num. of mol.: 2 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Strain: K12 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: P07013
#2: DNA chain 5'-D(*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP *TP*TP*TP*TP*T)-3'


Mass: 4517.935 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 119 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN A, GLY 103 TO VAL ENGINEERED RESIDUE IN CHAIN B, GLY 103 TO VAL
Has protein modificationY
Sequence detailsTHE RECOMBINANT FORM OF PRIB CONTAINS PARTIAL T7 TAG IN N- TERMINAL END, AND HIS TAG IN C-TERMINAL ...THE RECOMBINANT FORM OF PRIB CONTAINS PARTIAL T7 TAG IN N- TERMINAL END, AND HIS TAG IN C-TERMINAL END. GLY-103 IS REPLACED BY VAL.

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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: 1.8 Å3/Da / Density % sol: 31 %
Crystal growpH: 6.5 / Details: pH 6.50

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL17B2 / Wavelength: 1.12714
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Apr 30, 2005 / Details: MIRRORS
RadiationMonochromator: DCM WITH SAGITTAL FOCUSING / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.12714 Å / Relative weight: 1
ReflectionResolution: 2.7→20 Å / Num. obs: 6773 / % possible obs: 99.6 % / Observed criterion σ(I): 2 / Redundancy: 4.9 % / Biso Wilson estimate: 44 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 30.34
Reflection shellResolution: 2.7→2.8 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.42 / Mean I/σ(I) obs: 4.7 / % possible all: 100

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data reduction
HKL-2000data scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1V1Q

1v1q


Resolution: 2.7→17.6 Å / Rfactor Rfree error: 0.011 / Data cutoff high absF: 270117.32 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: 1. HIS-116 AND HIS-117 OF CHAIN A ARE INVISIBLE. 2. MET-6, ASP-5, HIS-115, HIS-116,HIS-117 OF CHAIN B ARE INVISIBLE. 3. THOSE SIDECHAINS LISTED AS FOLLOWS ARE DISORDERED CHAIN A MET-6, ASP- ...Details: 1. HIS-116 AND HIS-117 OF CHAIN A ARE INVISIBLE. 2. MET-6, ASP-5, HIS-115, HIS-116,HIS-117 OF CHAIN B ARE INVISIBLE. 3. THOSE SIDECHAINS LISTED AS FOLLOWS ARE DISORDERED CHAIN A MET-6, ASP-5, LEU-1, LEU-16, SER-20, GLN-45, ASN-59, HIS-81, MET-90, ILE-97, ILE-100, ASP-101, LEU- 106, HIS-112, HIS-114, HIS-115. CHAIN B SER-2, LEU-1, ASN-3, ILE-24, GLU-39, ILE-62, LEU-87, ASP-101, LYS-105, LEU-110.
RfactorNum. reflection% reflectionSelection details
Rfree0.284 664 10.8 %RANDOM
Rwork0.25 ---
obs0.25 6121 90.9 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 59.3093 Å2 / ksol: 0.241866 e/Å3
Displacement parametersBiso mean: 41 Å2
Baniso -1Baniso -2Baniso -3
1-6.67 Å20 Å20 Å2
2---6.32 Å20 Å2
3----0.35 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.4 Å0.36 Å
Luzzati d res low-5 Å
Luzzati sigma a0.37 Å0.4 Å
Refinement stepCycle: LAST / Resolution: 2.7→17.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1763 297 0 119 2179
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.012
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg2
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d30.5
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.47
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.331.5
X-RAY DIFFRACTIONc_mcangle_it2.292
X-RAY DIFFRACTIONc_scbond_it1.512
X-RAY DIFFRACTIONc_scangle_it2.312.5
LS refinement shellResolution: 2.7→2.87 Å / Rfactor Rfree error: 0.035 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.337 91 10.7 %
Rwork0.336 760 -
obs--76.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3ION.PARAMION.TOP
X-RAY DIFFRACTION4DNA-RNA_REP.PARAMDNA-RNA.TOP

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