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- PDB-1j1v: Crystal structure of DnaA domainIV complexed with DnaAbox DNA -

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Basic information

Entry
Database: PDB / ID: 1j1v
TitleCrystal structure of DnaA domainIV complexed with DnaAbox DNA
Components
  • 5'-D(*CP*CP*TP*GP*TP*GP*GP*AP*TP*AP*AP*CP*A)-3'
  • 5'-D(*TP*GP*TP*TP*AP*TP*CP*CP*AP*CP*AP*GP*G)-3'
  • Chromosomal replication initiator protein dnaA
Keywordsreplication/DNA / Protein-DNA complex / Replication / RIKEN Structural Genomics/Proteomics Initiative / RSGI / Structural Genomics / replication-DNA COMPLEX
Function / homology
Function and homology information


DnaA-oriC complex / DnaA-DiaA complex / DnaA-HU complex / DnaA-Dps complex / replication inhibiting complex / regulation of DNA-templated DNA replication initiation / DNA unwinding involved in DNA replication / positive regulation of DNA-templated DNA replication initiation / DNA replication origin binding / regulation of DNA replication ...DnaA-oriC complex / DnaA-DiaA complex / DnaA-HU complex / DnaA-Dps complex / replication inhibiting complex / regulation of DNA-templated DNA replication initiation / DNA unwinding involved in DNA replication / positive regulation of DNA-templated DNA replication initiation / DNA replication origin binding / regulation of DNA replication / DNA replication initiation / DnaA-L2 complex / negative regulation of DNA-templated DNA replication initiation / cytoplasmic side of plasma membrane / sequence-specific DNA binding / DNA replication / ATP hydrolysis activity / DNA binding / ATP binding / identical protein binding / plasma membrane / cytosol
Similarity search - Function
Chromosomal Replication Initiator Protein Dnaa; Chain: A; / DnaA protein, C-terminal DNA-binding domain / DnaA N-terminal domain / DnaA N-terminal domain / DnaA, N-terminal domain superfamily / Chromosomal replication control, initiator DnaA / Chromosomal replication initiator, DnaA C-terminal / Chromosomal replication control, initiator DnaA, conserved site / Bacterial dnaA protein helix-turn-helix / DnaA protein signature. ...Chromosomal Replication Initiator Protein Dnaa; Chain: A; / DnaA protein, C-terminal DNA-binding domain / DnaA N-terminal domain / DnaA N-terminal domain / DnaA, N-terminal domain superfamily / Chromosomal replication control, initiator DnaA / Chromosomal replication initiator, DnaA C-terminal / Chromosomal replication control, initiator DnaA, conserved site / Bacterial dnaA protein helix-turn-helix / DnaA protein signature. / Bacterial dnaA protein helix-turn-helix domain / Chromosomal replication control, initiator DnaA-like / Chromosomal replication initiator protein DnaA / Bacterial dnaA protein / Trp repressor/replication initiator / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
DNA / DNA (> 10) / Chromosomal replication initiator protein DnaA
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.1 Å
AuthorsFujikawa, N. / Kurumizaka, H. / Nureki, O. / Terada, T. / Shirouzu, M. / Katayama, T. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: NUCLEIC ACIDS RES. / Year: 2003
Title: Structural basis of replication origin recognition by the DnaA protein
Authors: Fujikawa, N. / Kurumizaka, H. / Nureki, O. / Terada, T. / Shirouzu, M. / Katayama, T. / Yokoyama, S.
History
DepositionDec 18, 2002Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 22, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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

Downloads & links

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Assembly

Deposited unit
B: 5'-D(*TP*GP*TP*TP*AP*TP*CP*CP*AP*CP*AP*GP*G)-3'
C: 5'-D(*CP*CP*TP*GP*TP*GP*GP*AP*TP*AP*AP*CP*A)-3'
A: Chromosomal replication initiator protein dnaA


Theoretical massNumber of molelcules
Total (without water)18,7763
Polymers18,7763
Non-polymers00
Water2,576143
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)50.385, 50.385, 158.830
Angle α, β, γ (deg.)90, 90, 90
Int Tables number92
Space group name H-MP41212

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Components

#1: DNA chain 5'-D(*TP*GP*TP*TP*AP*TP*CP*CP*AP*CP*AP*GP*G)-3' / DnaAbox DNA


Mass: 3966.597 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: DNA chain 5'-D(*CP*CP*TP*GP*TP*GP*GP*AP*TP*AP*AP*CP*A)-3' / DnaAbox DNA


Mass: 3975.611 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: Protein Chromosomal replication initiator protein dnaA


Mass: 10834.071 Da / Num. of mol.: 1 / Fragment: DNA binding domain, DnaA domainIV
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Description: cell-free protein synthesis system / Gene: DnaA / Plasmid: pET15b / References: UniProt: P03004
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 143 / 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: 2.53 Å3/Da / Density % sol: 51.04 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.4
Details: Tris-HCl, magnesium formate, polyethylene glycol 8000, pH 8.4, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Components of the solutions
IDNameCrystal-IDSol-ID
1Tris-HClTris11
2magnesium formate11
3polyethylene glycol 800011
4Tris-HClTris12
5magnesium formate12
6polyethylene glycol 800012
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
15 mg/mlprotein1drop
20.1 MTris-HCl1reservoirpH8.4
30.2 Mmagnesium formate1reservoir
418 %PEG80001reservoir
51
61

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 0.9792, 0.9795, 0.9840, 0.9736
DetectorType: MARRESEARCH / Detector: CCD / Date: Oct 26, 2002
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97921
20.97951
30.9841
40.97361
ReflectionResolution: 2.1→50 Å / Num. obs: 12618 / % possible obs: 99.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 2.1→2.18 Å / % possible all: 87.6
Reflection
*PLUS
Lowest resolution: 50 Å / % possible obs: 99 % / Redundancy: 12.5 % / Rmerge(I) obs: 0.055
Reflection shell
*PLUS
% possible obs: 98.8 % / Rmerge(I) obs: 0.11 / Mean I/σ(I) obs: 20.6

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
SHARPphasing
CNS1refinement
RefinementMethod to determine structure: MAD / Resolution: 2.1→50 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.2489 1303 RANDOM
Rwork0.2292 --
all0.2292 12685 -
obs0.2292 12599 -
Refine analyze
FreeObs
Luzzati coordinate error0.29 Å0.27 Å
Luzzati d res low-5 Å
Luzzati sigma a0.19 Å0.18 Å
Refinement stepCycle: LAST / Resolution: 2.1→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms752 527 0 143 1422
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_d1.15348
X-RAY DIFFRACTIONc_bond_d0.009139
X-RAY DIFFRACTIONc_dihedral_angle_d17.40347
X-RAY DIFFRACTIONc_improper_angle_d1.23851
LS refinement shell
Resolution (Å)Rfactor RfreeRfactor RworkRefine-IDTotal num. of bins used
2.1-2.180.24930.2466X-RAY DIFFRACTION6
2.18-2.260.24630.235X-RAY DIFFRACTION6
2.26-2.370.27890.2482X-RAY DIFFRACTION6
2.37-2.490.27540.2566X-RAY DIFFRACTION6
2.49-2.650.26510.2425X-RAY DIFFRACTION6
2.65-2.850.25970.2496X-RAY DIFFRACTION6
Refinement
*PLUS
Lowest resolution: 50 Å / % reflection Rfree: 10 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.0091
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_deg1.15
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg17.4
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.24

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