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- PDB-1v1q: Crystal structure of PriB- a primosomal DNA replication protein o... -

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Basic information

Entry
Database: PDB / ID: 1v1q
TitleCrystal structure of PriB- a primosomal DNA replication protein of Escherichia coli
ComponentsPRIMOSOMAL REPLICATION PROTEIN N
KeywordsDNA BINDING / PRIMOSOME / DNA REPLICATION
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
CYSTEINE / Primosomal replication protein N
Similarity search - Component
Biological speciesESCHERICHIA COLI (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.1 Å
AuthorsLiu, J.-H. / Chang, T.-W. / Huang, C.-Y. / Chang, M.-C. / Chen, S.-U. / Wu, H.-N. / Hsiao, C.-D.
CitationJournal: J.Biol.Chem. / Year: 2004
Title: Crystal Structure of Prib- a Primosomal DNA Replication Protein of Escherichia Coli
Authors: Liu, J.-H. / Chang, T.-W. / Huang, C.-Y. / Chen, S.-U. / Wu, H.-N. / Chang, M.-C. / Hsiao, C.-D.
History
DepositionApr 22, 2004Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 25, 2004Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_conn / struct_conn_type / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 11-STRANDED BARREL THIS IS REPRESENTED BY A 12-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL.

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,9475
Polymers29,5842
Non-polymers3633
Water2,414134
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)39.322, 57.358, 97.019
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


Mass: 14791.990 Da / Num. of mol.: 2 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Strain: K12 / Plasmid: PET21B-PRIB / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P07013
#2: Chemical ChemComp-CYS / CYSTEINE / Cysteine


Type: L-peptide linking / Mass: 121.158 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H7NO2S
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 134 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED MUTATION GLY 103 VAL
Sequence detailsRESIDUES PRECEDING POSITION 1 OF EACH MOLECULE ARE FROM T7-TAG, AND RESIDUES AFTER POSITION 104 OF ...RESIDUES PRECEDING POSITION 1 OF EACH MOLECULE ARE FROM T7-TAG, AND RESIDUES AFTER POSITION 104 OF CHAIN A ARE FROM HIS-TAG

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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: 1.9 Å3/Da / Density % sol: 33.7 %
Crystal growpH: 5.7 / Details: pH 5.70

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL17B2 / Wavelength: 1.0083, 1.0093, 0.9921, 1.0249
DetectorType: RIGAKU IMAGE PLATE / Detector: IMAGE PLATE / Details: MIRRORS
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.00831
21.00931
30.99211
41.02491
ReflectionResolution: 2.1→23.17 Å / Num. obs: 13751 / % possible obs: 99.9 % / Observed criterion σ(I): 2 / Redundancy: 3.6 % / Biso Wilson estimate: 13.9 Å2 / Rmerge(I) obs: 0.083 / Net I/σ(I): 14.1
Reflection shellResolution: 2.1→2.2 Å / Rmerge(I) obs: 0.561 / Mean I/σ(I) obs: 2.2 / % possible all: 99.6

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Processing

Software
NameVersionClassification
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 2.1→23.17 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 284509.74 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.263 1092 10.2 %RANDOM
Rwork0.206 ---
obs0.206 10679 79.9 %-
Solvent computationSolvent model: FLAT / Bsol: 40.8918 Å2 / ksol: 0.312944 e/Å3
Displacement parametersBiso mean: 40.1 Å2
Baniso -1Baniso -2Baniso -3
1-8.86 Å20 Å20 Å2
2---6.54 Å20 Å2
3----2.32 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.32 Å0.24 Å
Luzzati d res low-5 Å
Luzzati sigma a0.2 Å0.19 Å
Refinement stepCycle: LAST / Resolution: 2.1→23.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1704 0 21 134 1859
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
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_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d26.7
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.74
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.931.5
X-RAY DIFFRACTIONc_mcangle_it3.432
X-RAY DIFFRACTIONc_scbond_it1.862
X-RAY DIFFRACTIONc_scangle_it2.892.5
LS refinement shellResolution: 2.1→2.23 Å / Rfactor Rfree error: 0.026 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.29 122 9.6 %
Rwork0.228 1147 -
obs--58.4 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP

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