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- PDB-3fmt: Crystal structure of SeqA bound to DNA -

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Basic information

Entry
Database: PDB / ID: 3fmt
TitleCrystal structure of SeqA bound to DNA
Components
  • 5'-D(*GP*AP*GP*TP*CP*GP*(6MA)P*TP*CP*GP*GP*CP*GP*GP*GP*(6MA)P*TP*CP*CP*TP*TP*A)-3'
  • 5'-D(*TP*CP*TP*AP*AP*GP*GP*AP*TP*CP*CP*CP*GP*CP*CP*GP*AP*TP*CP*GP*AP*C)-3'
  • Protein seqA
KeywordsREPLICATION INHIBITOR/DNA / protein-DNA complex / hemimethylated GATC / DNA replication / sequestration / DNA replication inhibitor / DNA-binding / 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 / Met repressor-like / Arc Repressor Mutant ...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 / Met repressor-like / Arc Repressor Mutant / Arc-type ribbon-helix-helix / Ribbon-helix-helix / Up-down Bundle / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
DNA / DNA (> 10) / Negative modulator of initiation of replication
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.983 Å
AuthorsChung, Y.S. / Brendler, T. / Austin, S. / Guarne, A.
Citation
Journal: Nucleic Acids Res. / Year: 2009
Title: Structural insights into the cooperative binding of SeqA to a tandem GATC repeat
Authors: Chung, Y.S. / Brendler, T. / Austin, S. / Guarne, A.
#1: Journal: Acta Crystallogr.,Sect.F / Year: 2008
Title: Crystallization and preliminary X-ray diffraction analysis of SeqA bound to a pair of hemimethylated GATC sites
Authors: Chung, Y.S. / Guarne, A.
History
DepositionDec 22, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 28, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jul 26, 2017Group: Refinement description / Source and taxonomy / Category: entity_src_gen / software
Revision 1.3Oct 20, 2021Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / struct_conn / 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_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Sep 6, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Protein seqA
B: Protein seqA
C: 5'-D(*GP*AP*GP*TP*CP*GP*(6MA)P*TP*CP*GP*GP*CP*GP*GP*GP*(6MA)P*TP*CP*CP*TP*TP*A)-3'
D: 5'-D(*TP*CP*TP*AP*AP*GP*GP*AP*TP*CP*CP*CP*GP*CP*CP*GP*AP*TP*CP*GP*AP*C)-3'
E: Protein seqA
F: Protein seqA
G: 5'-D(*GP*AP*GP*TP*CP*GP*(6MA)P*TP*CP*GP*GP*CP*GP*GP*GP*(6MA)P*TP*CP*CP*TP*TP*A)-3'
H: 5'-D(*TP*CP*TP*AP*AP*GP*GP*AP*TP*CP*CP*CP*GP*CP*CP*GP*AP*TP*CP*GP*AP*C)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)101,70612
Polymers101,2338
Non-polymers4734
Water55831
1
A: Protein seqA
B: Protein seqA
C: 5'-D(*GP*AP*GP*TP*CP*GP*(6MA)P*TP*CP*GP*GP*CP*GP*GP*GP*(6MA)P*TP*CP*CP*TP*TP*A)-3'
D: 5'-D(*TP*CP*TP*AP*AP*GP*GP*AP*TP*CP*CP*CP*GP*CP*CP*GP*AP*TP*CP*GP*AP*C)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,8536
Polymers50,6174
Non-polymers2362
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10620 Å2
ΔGint-47 kcal/mol
Surface area22040 Å2
MethodPISA
2
E: Protein seqA
F: Protein seqA
G: 5'-D(*GP*AP*GP*TP*CP*GP*(6MA)P*TP*CP*GP*GP*CP*GP*GP*GP*(6MA)P*TP*CP*CP*TP*TP*A)-3'
H: 5'-D(*TP*CP*TP*AP*AP*GP*GP*AP*TP*CP*CP*CP*GP*CP*CP*GP*AP*TP*CP*GP*AP*C)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,8536
Polymers50,6174
Non-polymers2362
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10610 Å2
ΔGint-48 kcal/mol
Surface area22060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)121.839, 121.839, 279.133
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
12
22
13
23
14
24

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111chain B resid 1:162
211chain F resid 1:162
112chain A resid 1:162
212chain E resid 1:162
113chain D resid 1:22
213chain H resid 1:22
114chain C resid 1:22
214chain G resid 1:22

NCS ensembles :
ID
1
2
3
4

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Components

#1: Protein
Protein seqA


Mass: 18541.377 Da / Num. of mol.: 4 / Fragment: SeqAdelta(41-59) / Mutation: A25R, deletion 41-59
Source method: isolated from a genetically manipulated source
Details: SeqA with a point mutation A25R and linker deletion (residues 41-59)
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K-12 / Gene: b0687, JW0674, seqA / Plasmid: pET11a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P0AFY8
#2: DNA chain 5'-D(*GP*AP*GP*TP*CP*GP*(6MA)P*TP*CP*GP*GP*CP*GP*GP*GP*(6MA)P*TP*CP*CP*TP*TP*A)-3'


Mass: 6836.441 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: methylated oligonucleotide
#3: DNA chain 5'-D(*TP*CP*TP*AP*AP*GP*GP*AP*TP*CP*CP*CP*GP*CP*CP*GP*AP*TP*CP*GP*AP*C)-3'


Mass: 6697.331 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: unmethylated oligonucleotide
#4: Chemical
ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 31 / 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: 3.98 Å3/Da / Density % sol: 69.07 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 18% MPD, 0.4 M ammonium acetate, 0.1 M sodium citrate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Components of the solutions
IDNameCrystal-IDSol-ID
1MPD11
2ammonium acetate11
3sodium citrate11
4MPD12
5ammonium acetate12
6sodium citrate12

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 27, 2007 / Details: mirrors
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.98→35.17 Å / Num. all: 30853 / Num. obs: 30745 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.2 % / Biso Wilson estimate: 76.39 Å2 / Rmerge(I) obs: 0.088 / Rsym value: 0.067 / Net I/σ(I): 13.5
Reflection shellResolution: 2.98→3.11 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.527 / Mean I/σ(I) obs: 1.8 / Rsym value: 0.457 / % possible all: 100

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Processing

Software
NameVersionClassification
CBASSdata collection
PHASERphasing
PHENIX(phenix.refine)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1LRR and 1XRX

1lrr

1xrx


Resolution: 2.983→35.172 Å / SU ML: 1.83 / Isotropic thermal model: group / σ(F): 1.98 / Phase error: 25.77 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2448 1533 5.06 %
Rwork0.2181 --
obs0.2194 30285 96.33 %
all-30853 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 27.555 Å2 / ksol: 0.297 e/Å3
Refinement stepCycle: LAST / Resolution: 2.983→35.172 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5142 1758 0 63 6963
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0047226
X-RAY DIFFRACTIONf_angle_d0.87710104
X-RAY DIFFRACTIONf_dihedral_angle_d14.7613088
X-RAY DIFFRACTIONf_chiral_restr0.0491140
X-RAY DIFFRACTIONf_plane_restr0.003976
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11B1274X-RAY DIFFRACTIONPOSITIONAL
12F1274X-RAY DIFFRACTIONPOSITIONAL0.035
21A1297X-RAY DIFFRACTIONPOSITIONAL
22E1297X-RAY DIFFRACTIONPOSITIONAL0.003
31D425X-RAY DIFFRACTIONPOSITIONAL
32H425X-RAY DIFFRACTIONPOSITIONAL0.003
41C454X-RAY DIFFRACTIONPOSITIONAL
42G454X-RAY DIFFRACTIONPOSITIONAL0.003
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9832-3.07950.37451040.31621847X-RAY DIFFRACTION69
3.0795-3.18950.26391380.30882482X-RAY DIFFRACTION92
3.1895-3.31710.30811560.25722725X-RAY DIFFRACTION99
3.3171-3.46790.31711370.25082708X-RAY DIFFRACTION100
3.4679-3.65060.28391210.23282750X-RAY DIFFRACTION100
3.6506-3.8790.23731530.22682670X-RAY DIFFRACTION100
3.879-4.17810.22961600.20212714X-RAY DIFFRACTION100
4.1781-4.59770.18741280.18572706X-RAY DIFFRACTION100
4.5977-5.26110.23181360.18712761X-RAY DIFFRACTION100
5.2611-6.62120.23561580.20972677X-RAY DIFFRACTION100
6.6212-35.17430.17951420.16742712X-RAY DIFFRACTION99

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