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- PDB-1txy: E. coli PriB -

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Basic information

Entry
Database: PDB / ID: 1txy
TitleE. coli PriB
ComponentsPrimosomal replication protein n
KeywordsDNA BINDING PROTEIN / OB fold / dimer
Function / homology
Function and homology information


pre-primosome complex / DnaB-DnaC-DnaT-PriA-PriB complex / plasmid maintenance / primosome complex / DNA replication, synthesis of primer / DNA unwinding involved in DNA replication / replication fork processing / DNA replication initiation / response to radiation / single-stranded DNA 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
Primosomal replication protein N
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2 Å
AuthorsKeck, J.L. / Lopper, M. / Holton, J.M.
CitationJournal: Structure / Year: 2004
Title: Crystal structure of PriB, a component of the Escherichia coli replication restart primosome
Authors: Lopper, M. / Holton, J.M. / Keck, J.L.
History
DepositionJul 6, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 16, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Refinement description / Version format compliance
Revision 1.3Nov 6, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details

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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


Theoretical massNumber of molelcules
Total (without water)23,2002
Polymers23,2002
Non-polymers00
Water2,522140
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2710 Å2
ΔGint-21 kcal/mol
Surface area9460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.902, 60.294, 66.304
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: 11599.880 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: PRIB, B4201 / Production host: Escherichia coli (E. coli) / References: UniProt: P07013
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 140 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.13 Å3/Da / Density % sol: 41 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: PEG 8000, Tris-HCl, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.0200, 0.9798, 0.9797
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 10, 2004
RadiationMonochromator: Double crystal / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.021
20.97981
30.97971
ReflectionResolution: 2→34 Å / Num. all: 16070 / Num. obs: 16070 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 2→2.1 Å / % possible all: 99.8

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Processing

Software
NameVersionClassification
REFMAC5refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 2→20 Å / Cor.coef. Fo:Fc: 0.913 / Cor.coef. Fo:Fc free: 0.903 / SU B: 5.173 / SU ML: 0.149 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.241 / ESU R Free: 0.196 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.28485 693 5 %RANDOM
Rwork0.25884 ---
all0.26009 13288 --
obs0.26009 13288 99.72 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 22.371 Å2
Baniso -1Baniso -2Baniso -3
1--1.01 Å20 Å20 Å2
2---0.16 Å20 Å2
3---1.18 Å2
Refinement stepCycle: LAST / Resolution: 2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1375 0 0 140 1515
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0211401
X-RAY DIFFRACTIONr_angle_refined_deg1.1471.9111890
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.1883171
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.49315252
X-RAY DIFFRACTIONr_chiral_restr0.080.2219
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021028
X-RAY DIFFRACTIONr_nbd_refined0.2920.3623
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1720.5174
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3170.340
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2260.58
X-RAY DIFFRACTIONr_mcbond_it0.8741.5871
X-RAY DIFFRACTIONr_mcangle_it1.51121413
X-RAY DIFFRACTIONr_scbond_it2.4173530
X-RAY DIFFRACTIONr_scangle_it3.7394.5477
LS refinement shellResolution: 2→2.051 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.248 47
Rwork0.264 940
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.41191.5780.2032.4406-0.56561.397-0.0636-0.03440.0904-0.04990.09290.10970.0717-0.0644-0.02930.10150.0045-0.02390.07030.0210.04631.06513.34449.777
24.86561.7927-1.02674.3834-1.66013.79730.0035-0.3428-0.26760.0658-0.3306-0.6679-0.03790.19910.32710.0341-0.011-0.04860.0780.07360.114148.88583.789816.6422
33.48610.46110.37831.4136-1.07051.17330.0812-0.0347-0.0099-0.0142-0.05840.01810.0662-0.0529-0.02280.1407-0.0163-0.02010.0847-0.02190.090938.26593.321512.1433
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 100
2X-RAY DIFFRACTION2B1 - 98
3X-RAY DIFFRACTION3A105 - 190
4X-RAY DIFFRACTION3B105 - 158

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