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- PDB-1j3e: Crystal Structure of the E.coli SeqA protein complexed with N6-me... -

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Basic information

Entry
Database: PDB / ID: 1j3e
TitleCrystal Structure of the E.coli SeqA protein complexed with N6-methyladenine- guanine mismatch DNA
Components
  • 5'-D(*AP*AP*GP*GP*(6MA)P*TP*CP*CP*AP*A)-3'
  • 5'-D(*TP*TP*GP*GP*AP*GP*CP*CP*TP*T)-3'
  • SeqA protein
KeywordsREPLICATION/DNA / Protein-DNA complex / Recognition of hemimethylated DNA / mismatched DNA / replication / RIKEN Structural Genomics/Proteomics Initiative / RSGI / Structural Genomics / REPLICATION-DNA COMPLEX
Function / homology
Function and homology information


SeqA-DNA complex / nucleoid organization / double-stranded methylated DNA binding / hemi-methylated DNA-binding / sister chromatid cohesion / DNA replication origin binding / negative regulation of DNA-templated DNA replication initiation / response to radiation / regulation of DNA-templated transcription / protein homodimerization activity ...SeqA-DNA complex / nucleoid organization / double-stranded methylated DNA binding / hemi-methylated DNA-binding / sister chromatid cohesion / DNA replication origin binding / negative regulation of DNA-templated DNA replication initiation / response to radiation / regulation of DNA-templated transcription / protein homodimerization activity / protein-containing complex / identical protein binding / cytosol
Similarity search - Function
Replication modulator SeqA, C-terminal DNA-binding domain / Replication modulator SeqA, C-terminal DNA-binding domain / Negative modulator of initiation of replication SeqA / Replication modulator SeqA, C-terminal DNA-binding domain / Negative modulator of initiation of replication SeqA, N-terminal / Replication modulator SeqA, C-terminal DNA-binding domain superfamily / SeqA protein C-terminal domain / SeqA protein N-terminal domain / Arc-type ribbon-helix-helix / Ribbon-helix-helix ...Replication modulator SeqA, C-terminal DNA-binding domain / Replication modulator SeqA, C-terminal DNA-binding domain / Negative modulator of initiation of replication SeqA / Replication modulator SeqA, C-terminal DNA-binding domain / Negative modulator of initiation of replication SeqA, N-terminal / Replication modulator SeqA, C-terminal DNA-binding domain superfamily / SeqA protein C-terminal domain / SeqA protein N-terminal domain / Arc-type ribbon-helix-helix / Ribbon-helix-helix / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
DNA / Negative modulator of initiation of replication / Negative modulator of initiation of replication
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsFujikawa, N. / Kurumizaka, H. / Nureki, O. / Tanaka, Y. / Yamazoe, M. / Hiraga, S. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: Nucleic Acids Res. / Year: 2004
Title: Structural and biochemical analyses of hemimethylated DNA binding by the SeqA protein
Authors: Fujikawa, N. / Kurumizaka, H. / Nureki, O. / Tanaka, Y. / Yamazoe, M. / Hiraga, S. / Yokoyama, S.
History
DepositionJan 24, 2003Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 18, 2004Provider: 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(*AP*AP*GP*GP*(6MA)P*TP*CP*CP*AP*A)-3'
C: 5'-D(*TP*TP*GP*GP*AP*GP*CP*CP*TP*T)-3'
A: SeqA protein


Theoretical massNumber of molelcules
Total (without water)19,1063
Polymers19,1063
Non-polymers00
Water1,51384
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)33.432, 65.061, 77.176
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: DNA chain 5'-D(*AP*AP*GP*GP*(6MA)P*TP*CP*CP*AP*A)-3'


Mass: 3076.071 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: DNA chain 5'-D(*TP*TP*GP*GP*AP*GP*CP*CP*TP*T)-3'


Mass: 3051.002 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: Protein SeqA protein /


Mass: 12978.878 Da / Num. of mol.: 1 / Fragment: DNA binding domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: SeqA / Plasmid: pGEX6P-1 / Production host: Escherichia coli (E. coli) / Strain (production host): DH5a / References: UniProt: P36658, UniProt: P0AFY8*PLUS
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 84 / 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: 2.18 Å3/Da / Density % sol: 43.06 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: Ca-acetate, Na-cacodylate, PEG8K, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Components of the solutions
IDNameCrystal-IDSol-ID
1PEG 800011
2Ca-acetate11
3Na-cacodylate11
4PEG 800012
5Ca-acetate12
6Na-cacodylate12

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 0.974 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Oct 26, 2002
RadiationMonochromator: rotated-inclined fixed exit double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.974 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. all: 6296 / Num. obs: 6126 / % possible obs: 97.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 2.5→2.59 Å / % possible all: 94.9

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNS1refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→40 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.296 343 RANDOM
Rwork0.2302 --
obs0.2302 6094 -
all-6228 -
Refine analyze
FreeObs
Luzzati coordinate error0.5 Å0.35 Å
Luzzati d res low-5 Å
Luzzati sigma a0.52 Å0.44 Å
Refinement stepCycle: LAST / Resolution: 2.5→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms908 407 0 84 1399
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_bond_d0.00983
X-RAY DIFFRACTIONc_dihedral_angle_d19.7
X-RAY DIFFRACTIONc_improper_angle_d1.41
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkRefine-IDTotal num. of bins used
2.5-2.590.415400.3552X-RAY DIFFRACTION6
2.59-2.690.3946330.3257X-RAY DIFFRACTION6
2.69-2.820.4517300.3126X-RAY DIFFRACTION6
2.82-2.960.4306260.2962X-RAY DIFFRACTION6
2.96-3.150.331330.2687X-RAY DIFFRACTION6
3.15-3.390.2335450.2175X-RAY DIFFRACTION6

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