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- PDB-2z9o: Crystal structure of the dimeric form of RepE in complex with the... -

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Basic information

Entry
Database: PDB / ID: 2z9o
TitleCrystal structure of the dimeric form of RepE in complex with the repE operator DNA
Components
  • (DNA (33-MER)) x 2
  • Replication initiation protein
KeywordsREPLICATION/DNA / REPLICATION INITIATOR / AUTOGENOUS REPRESSOR / PROTEIN-DNA COMPLEX / WINGED HELIX-TURN-HELIX / DNA replication / DNA-binding / REPLICATION-DNA COMPLEX
Function / homology
Function and homology information


plasmid maintenance / DNA replication initiation / DNA-directed DNA polymerase activity / DNA binding
Similarity search - Function
Initiator Rep protein / Initiator Replication protein, WH1 / Initiator Rep protein, WH2 / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
DNA / DNA (> 10) / Replication initiation protein
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.14 Å
AuthorsNakamura, A. / Wada, C. / Miki, K.
CitationJournal: Proc.Natl.Acad.Sci.Usa / Year: 2007
Title: Structural basis for regulation of bifunctional roles in replication initiator protein
Authors: Nakamura, A. / Wada, C. / Miki, K.
History
DepositionSep 21, 2007Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 27, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.2Nov 1, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq.db_align_beg / _struct_ref_seq.db_align_end / _struct_ref_seq_dif.details
Remark 650HELIX DETERMINATION METHOD: AUTHOR DETERMINED
Remark 700SHEET DETERMINATION METHOD: AUTHOR DETERMINED

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
C: DNA (33-MER)
D: DNA (33-MER)
A: Replication initiation protein
B: Replication initiation protein


Theoretical massNumber of molelcules
Total (without water)82,5644
Polymers82,5644
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.729, 99.316, 95.003
Angle α, β, γ (deg.)90.00, 108.55, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: DNA chain DNA (33-MER)


Mass: 10087.534 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: DNA chain DNA (33-MER)


Mass: 10207.605 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: Protein Replication initiation protein / Protein rep / Protein E / Protein F4


Mass: 31134.457 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: repE / Plasmid: pQE-9 / Production host: Escherichia coli (E. coli) / Strain (production host): M15 / References: UniProt: P03856

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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: 3.29 Å3/Da / Density % sol: 62.61 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.2
Details: 10% PEG 4000, 200mM Sodium Chloride, 5mM Samarium Chloride, 100mM HEPES-NaOH, pH 7.2, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Components of the solutions
IDNameCrystal-IDSol-ID
1PEG 400011
2Sodium Chloride11
3Samarium Chloride11
4HEPES-NaOH11
5PEG 400012
6Sodium Chloride12
7Samarium Chloride12
8HEPES-NaOH12

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 26, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.14→50 Å / Num. obs: 16535 / % possible obs: 88.3 % / Observed criterion σ(I): 0 / Redundancy: 2.6 % / Biso Wilson estimate: 23 Å2 / Rsym value: 0.067 / Net I/σ(I): 11
Reflection shellResolution: 3.14→3.25 Å / Mean I/σ(I) obs: 3.9 / Rsym value: 0.15 / % possible all: 73.6

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Processing

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

1rep


Resolution: 3.14→45.03 Å / Rfactor Rfree error: 0.011 / Data cutoff high absF: 276022.34 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.313 850 5.1 %RANDOM
Rwork0.266 ---
obs0.266 16519 87.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 10.4121 Å2 / ksol: 0.198433 e/Å3
Displacement parametersBiso mean: 45.7 Å2
Baniso -1Baniso -2Baniso -3
1-38.31 Å20 Å2-7.15 Å2
2---10.08 Å20 Å2
3----28.23 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.56 Å0.43 Å
Luzzati d res low-5 Å
Luzzati sigma a0.65 Å0.75 Å
Refinement stepCycle: LAST / Resolution: 3.14→45.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3579 1347 0 0 4926
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.008
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_d22.1
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.481.5
X-RAY DIFFRACTIONc_mcangle_it2.642
X-RAY DIFFRACTIONc_scbond_it1.672
X-RAY DIFFRACTIONc_scangle_it2.832.5
LS refinement shellResolution: 3.14→3.34 Å / Rfactor Rfree error: 0.037 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.4 119 5.3 %
Rwork0.364 2136 -
obs--72.4 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3dna-rna_rep.paramdna-rna.top

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