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- PDB-1iu3: CRYSTAL STRUCTURE OF THE E.COLI SEQA PROTEIN COMPLEXED WITH HEMIM... -

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Basic information

Entry
Database: PDB / ID: 1iu3
TitleCRYSTAL STRUCTURE OF THE E.COLI SEQA PROTEIN COMPLEXED WITH HEMIMETHYLATED DNA
Components
  • 5'-D(*AP*AP*GP*GP*AP*TP*CP*CP*AP*A)-3'
  • 5'-D(*TP*TP*GP*GP*AP*TP*CP*CP*TP*T)-3'
  • SeqA protein
KeywordsREPLICATION INHIBITOR/DNA / Protein-DNA complex / Recognition of hemimethylated DNA / RIKEN Structural Genomics/Proteomics Initiative / RSGI / Structural Genomics / REPLICATION INHIBITOR-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 / MAD / Resolution: 3 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
DepositionFeb 26, 2002Deposition site: PDBJ / Processing site: RCSB
Revision 1.0Jun 17, 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
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 5'-D(*AP*AP*GP*GP*AP*TP*CP*CP*AP*A)-3'
B: 5'-D(*TP*TP*GP*GP*AP*TP*CP*CP*TP*T)-3'
D: 5'-D(*AP*AP*GP*GP*AP*TP*CP*CP*AP*A)-3'
E: 5'-D(*TP*TP*GP*GP*AP*TP*CP*CP*TP*T)-3'
C: SeqA protein
F: SeqA protein


Theoretical massNumber of molelcules
Total (without water)38,2486
Polymers38,2486
Non-polymers00
Water2,360131
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)152.595, 152.595, 119.355
Angle α, β, γ (deg.)90, 90, 120
Int Tables number177
Space group name H-MP622

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Components

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


Mass: 3062.044 Da / Num. of mol.: 2 / Source method: obtained synthetically
#2: DNA chain 5'-D(*TP*TP*GP*GP*AP*TP*CP*CP*TP*T)-3'


Mass: 3025.989 Da / Num. of mol.: 2 / Source method: obtained synthetically
#3: Protein SeqA protein


Mass: 13035.929 Da / Num. of mol.: 2 / Fragment: DNA binding domain, Residues 71-181
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: SeqA / Plasmid: pGEX-6P1 / Production host: Escherichia coli (E. coli) / Strain (production host): DH5a / References: UniProt: P36658, UniProt: P0AFY8*PLUS
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 131 / 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: 2

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Sample preparation

CrystalDensity Matthews: 5.24 Å3/Da / Density % sol: 76.54 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: HEPES-Na, tri-Sodium Citrate dihydrate, Glycerol, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Components of the solutions
IDNameCrystal-IDSol-ID
1HEPES-Na11
2tri-Sodium Citrate dihydrate11
3Glycerol11
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
15 mg/mlprotein1drop
290 mMHEPES1reservoirpH7.5
31.26 Mtri-sodium citrate dihydrate1reservoir
410 %glycerol1reservoir

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONSPring-8 BL41XU10.979713
SYNCHROTRONSPring-8 BL41XU20.9798,0.9800,0.9742,0.9839
Detector
TypeIDDetectorDate
MARRESEARCH1CCDJan 1, 2001
MARRESEARCH2CCDJan 1, 2001
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1rotated-inclined fixed exit double crystalSINGLE WAVELENGTHMx-ray1
2rotated-inclined fixed exit double crystalMADMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.9797131
20.97981
30.981
40.97421
50.98391
ReflectionResolution: 3→41.33 Å / Num. all: 16587 / Num. obs: 16587 / % possible obs: 98.5 % / Observed criterion σ(I): 0
Reflection shellResolution: 3→3.05 Å / % possible all: 85.4
Reflection
*PLUS
Lowest resolution: 50 Å / Num. obs: 16548 / Redundancy: 11.6 % / Rmerge(I) obs: 0.072
Reflection shell
*PLUS
% possible obs: 95.9 % / Rmerge(I) obs: 0.4 / Mean I/σ(I) obs: 2.2

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
MLPHAREphasing
CNS1refinement
RefinementMethod to determine structure: MAD / Resolution: 3→40 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.286 816 RANDOM
Rwork0.238 --
all-16587 -
obs-16586 -
Refine analyze
FreeObs
Luzzati coordinate error0.54 Å0.41 Å
Luzzati d res low-5 Å
Luzzati sigma a0.82 Å0.69 Å
Refinement stepCycle: LAST / Resolution: 3→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1816 808 0 131 2755
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_d3.16095
X-RAY DIFFRACTIONc_bond_d0.0316
X-RAY DIFFRACTIONc_dihedral_angle_d22.82394
X-RAY DIFFRACTIONc_improper_angle_d2.6685
LS refinement shell
Resolution (Å)Rfactor RworkRefine-IDTotal num. of bins used
3-3.050.523X-RAY DIFFRACTION6
3.05-3.110.496X-RAY DIFFRACTION6
3.11-3.170.476X-RAY DIFFRACTION6
3.17-3.230.376X-RAY DIFFRACTION6
3.23-3.30.302X-RAY DIFFRACTION6
3.3-3.380.284X-RAY DIFFRACTION6
Refinement
*PLUS
% reflection Rfree: 10 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.032
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_deg3.16
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg22.8
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg2.67

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