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- PDB-3vw4: Crystal structure of the DNA-binding domain of ColE2-P9 Rep in co... -

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Basic information

Entry
Database: PDB / ID: 3vw4
TitleCrystal structure of the DNA-binding domain of ColE2-P9 Rep in complex with the replication origin
Components
  • DNA (5'-D(P*AP*AP*TP*GP*AP*GP*AP*CP*CP*AP*GP*AP*TP*AP*AP*GP*CP*CP*TP*TP*AP*TP*C)-3')
  • DNA (5'-D(P*GP*AP*TP*AP*AP*GP*GP*CP*TP*TP*AP*TP*CP*TP*GP*GP*TP*CP*TP*CP*AP*TP*T)-3')
  • Rep
KeywordsDNA BINDING PROTEIN/DNA / helix-turn-helix / specific DNA-binding and unwinding of DNA duplex / cytosol / replication initiator protein / DNA BINDING PROTEIN-DNA complex
Function / homology
Function and homology information


sequence-specific DNA binding / regulation of DNA-templated transcription
Similarity search - Function
Endonuclease III; domain 1 - #50 / Plasmid replicase, bacterial / Primase, C-terminal 1 / Replicase family / Primase C terminal 1 (PriCT-1) / Met repressor-like / Arc Repressor Mutant / Arc-type ribbon-helix-helix / Endonuclease III; domain 1 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
DNA / DNA (> 10) / Rep
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.7 Å
AuthorsItou, H. / Yagura, M. / Itoh, T. / Shirakihara, Y.
CitationJournal: J.Biol.Chem. / Year: 2015
Title: Structural Basis for Replication Origin Unwinding by An Initiator-Primase of Plasmid ColE2-P9: Duplex DNA Unwinding by A Single Protein
Authors: Itou, H. / Yagura, M. / Shirakihara, Y. / Itoh, T.
History
DepositionJul 31, 2012Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 31, 2013Provider: repository / Type: Initial release
Revision 1.1Jan 28, 2015Group: Database references
Revision 1.2Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Rep
B: Rep
C: DNA (5'-D(P*AP*AP*TP*GP*AP*GP*AP*CP*CP*AP*GP*AP*TP*AP*AP*GP*CP*CP*TP*TP*AP*TP*C)-3')
D: DNA (5'-D(P*GP*AP*TP*AP*AP*GP*GP*CP*TP*TP*AP*TP*CP*TP*GP*GP*TP*CP*TP*CP*AP*TP*T)-3')
E: DNA (5'-D(P*AP*AP*TP*GP*AP*GP*AP*CP*CP*AP*GP*AP*TP*AP*AP*GP*CP*CP*TP*TP*AP*TP*C)-3')
F: DNA (5'-D(P*GP*AP*TP*AP*AP*GP*GP*CP*TP*TP*AP*TP*CP*TP*GP*GP*TP*CP*TP*CP*AP*TP*T)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,17311
Polymers57,6926
Non-polymers4805
Water48627
1
A: Rep
C: DNA (5'-D(P*AP*AP*TP*GP*AP*GP*AP*CP*CP*AP*GP*AP*TP*AP*AP*GP*CP*CP*TP*TP*AP*TP*C)-3')
D: DNA (5'-D(P*GP*AP*TP*AP*AP*GP*GP*CP*TP*TP*AP*TP*CP*TP*GP*GP*TP*CP*TP*CP*AP*TP*T)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,9424
Polymers28,8463
Non-polymers961
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7080 Å2
ΔGint-28 kcal/mol
Surface area12390 Å2
MethodPISA
2
B: Rep
E: DNA (5'-D(P*AP*AP*TP*GP*AP*GP*AP*CP*CP*AP*GP*AP*TP*AP*AP*GP*CP*CP*TP*TP*AP*TP*C)-3')
F: DNA (5'-D(P*GP*AP*TP*AP*AP*GP*GP*CP*TP*TP*AP*TP*CP*TP*GP*GP*TP*CP*TP*CP*AP*TP*T)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,2307
Polymers28,8463
Non-polymers3844
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7540 Å2
ΔGint-63 kcal/mol
Surface area12670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.662, 61.824, 273.508
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(-0.976328, 0.113415, -0.184178), (-0.113122, -0.993507, -0.01213), (-0.184358, 0.008991, 0.982818)43.76983, 37.72441, 4.07547

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Components

#1: Protein Rep / replication initiator ColE2-Rep


Mass: 14726.999 Da / Num. of mol.: 2 / Fragment: DNA-bindig domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: rep / Plasmid: pET28 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q06B24
#2: DNA chain DNA (5'-D(P*AP*AP*TP*GP*AP*GP*AP*CP*CP*AP*GP*AP*TP*AP*AP*GP*CP*CP*TP*TP*AP*TP*C)-3')


Mass: 7057.600 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: synthetic oligo DNA
#3: DNA chain DNA (5'-D(P*GP*AP*TP*AP*AP*GP*GP*CP*TP*TP*AP*TP*CP*TP*GP*GP*TP*CP*TP*CP*AP*TP*T)-3')


Mass: 7061.568 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: synthetic oligo DNA
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 27 / 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: 3.49 Å3/Da / Density % sol: 64.78 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 0.5M ammonium sulfate, 1.0M lithium sulfate, 0.1M sodium-citrate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 17, 2011 / Details: monochromator and mirrors
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.7→50 Å / Num. all: 23141 / Num. obs: 22951 / % possible obs: 99.5 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 6.4 % / Rmerge(I) obs: 0.133 / Net I/σ(I): 16.8
Reflection shellResolution: 2.7→2.75 Å / Redundancy: 6.5 % / Mean I/σ(I) obs: 5.1 / % possible all: 100

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
SOLVEphasing
REFMAC5.6.0117refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 2.7→40 Å / Cor.coef. Fo:Fc: 0.911 / Cor.coef. Fo:Fc free: 0.871 / SU B: 11.645 / SU ML: 0.191 / Cross valid method: THROUGHOUT / ESU R: 0.44 / ESU R Free: 0.298 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.26233 1168 5.1 %RANDOM
Rwork0.22014 ---
all0.26 23141 --
obs0.22232 21787 99.23 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 34.534 Å2
Baniso -1Baniso -2Baniso -3
1--0.83 Å20 Å2-0 Å2
2--2 Å20 Å2
3----1.18 Å2
Refinement stepCycle: LAST / Resolution: 2.7→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1972 1665 25 27 3689
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0153920
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.1931.6485644
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6275240
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.72319.7891
X-RAY DIFFRACTIONr_dihedral_angle_3_deg22.80115348
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.0661526
X-RAY DIFFRACTIONr_chiral_restr0.1280.2522
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.0212411
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.702→2.771 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.423 64 -
Rwork0.318 1376 -
obs--95.68 %
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)
14.7071-3.0529-1.3863.39632.13322.4524-0.0062-0.19590.0868-0.09930.0949-0.0492-0.1590.143-0.08860.0127-0.00620.00350.0330.00860.045329.92316.58174.732
27.01352.78260.609412.487313.830416.3296-0.54860.44830.18370.42470.7015-0.1210.85590.5646-0.15291.05180.0570.04030.74750.09420.242236.55712.9312.89
32.502-0.3408-0.15344.0656-2.33673.32130.0180.0194-0.0532-0.08920.04070.11920.149-0.1213-0.05880.0076-0.0083-0.0040.0264-0.00460.0372.87920.05372.203
40.81870.35511.81283.0009-4.605314.48010.05180.326-0.1289-0.05470.66860.25160.0127-0.0362-0.72040.9911-0.02070.06450.9948-0.05090.3389-0.76419.9111.774
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A175 - 239
2X-RAY DIFFRACTION2A269 - 290
3X-RAY DIFFRACTION3B175 - 239
4X-RAY DIFFRACTION4B269 - 290

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