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- PDB-1lrr: CRYSTAL STRUCTURE OF E. COLI SEQA COMPLEXED WITH HEMIMETHYLATED DNA -

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Basic information

Entry
Database: PDB / ID: 1lrr
TitleCRYSTAL STRUCTURE OF E. COLI SEQA COMPLEXED WITH HEMIMETHYLATED DNA
Components
  • 5'-D(*AP*GP*TP*CP*GP*(6MA)P*TP*CP*GP*GP*TP*G)-3'
  • 5'-D(*CP*AP*CP*CP*GP*AP*TP*CP*GP*AP*CP*T)-3'
  • SeqA protein
KeywordsREPLICATION INHIBITOR/DNA / protein-dna complex / replication / methylated GATC / 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 / DNA (> 10) / Negative modulator of initiation of replication / Negative modulator of initiation of replication
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.65 Å
AuthorsGuarne, A. / Zhao, Q. / Guirlando, R. / Yang, W.
CitationJournal: NAT.STRUCT.BIOL. / Year: 2002
Title: Insights into negative modulation of E. coli replication initiation from the structure of SeqA-hemimethylated DNA complex
Authors: Guarne, A. / Zhao, Q. / Guirlando, R. / Yang, W.
History
DepositionMay 15, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 11, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 29, 2013Group: Atomic model
Revision 1.4Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag
Revision 1.5Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: 5'-D(*CP*AP*CP*CP*GP*AP*TP*CP*GP*AP*CP*T)-3'
C: 5'-D(*AP*GP*TP*CP*GP*(6MA)P*TP*CP*GP*GP*TP*G)-3'
E: 5'-D(*CP*AP*CP*CP*GP*AP*TP*CP*GP*AP*CP*T)-3'
F: 5'-D(*AP*GP*TP*CP*GP*(6MA)P*TP*CP*GP*GP*TP*G)-3'
A: SeqA protein
D: SeqA protein


Theoretical massNumber of molelcules
Total (without water)44,2026
Polymers44,2026
Non-polymers00
Water66737
1
B: 5'-D(*CP*AP*CP*CP*GP*AP*TP*CP*GP*AP*CP*T)-3'
C: 5'-D(*AP*GP*TP*CP*GP*(6MA)P*TP*CP*GP*GP*TP*G)-3'
A: SeqA protein


Theoretical massNumber of molelcules
Total (without water)22,1013
Polymers22,1013
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
E: 5'-D(*CP*AP*CP*CP*GP*AP*TP*CP*GP*AP*CP*T)-3'
F: 5'-D(*AP*GP*TP*CP*GP*(6MA)P*TP*CP*GP*GP*TP*G)-3'
D: SeqA protein


Theoretical massNumber of molelcules
Total (without water)22,1013
Polymers22,1013
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)106.493, 106.493, 49.078
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number77
Space group name H-MP42

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Components

#1: DNA chain 5'-D(*CP*AP*CP*CP*GP*AP*TP*CP*GP*AP*CP*T)-3'


Mass: 3607.369 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: synthetic oligonuclotide
#2: DNA chain 5'-D(*AP*GP*TP*CP*GP*(6MA)P*TP*CP*GP*GP*TP*G)-3'


Mass: 3732.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: synthetic oligonuclotide
#3: Protein SeqA protein


Mass: 14761.073 Da / Num. of mol.: 2 / Fragment: Residues 51-181
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: seqA / Plasmid: pET11A / Production host: Escherichia coli (E. coli) / Strain (production host): BL834(DE3) / References: UniProt: P36658, UniProt: P0AFY8*PLUS
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 37 / 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: 3.07 Å3/Da / Density % sol: 59.6 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: PEG 4000, lithium sulphate, TRIS-HCl, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal grow
*PLUS
Temperature: 4 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
15 mg/mlprotein1drop
220-23 %(w/v)PEG40001reservoir
30.2 M1reservoirLi2SO4
40.1 MTris1reservoirpH8.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Apr 1, 2002 / Details: mirrors
RadiationMonochromator: Ni Filter / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.65→25 Å / Num. all: 16344 / Num. obs: 16187 / % possible obs: 99.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.2 % / Biso Wilson estimate: 71.9 Å2 / Rmerge(I) obs: 0.087 / Net I/σ(I): 14.6
Reflection shellResolution: 2.65→2.7 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.355 / Mean I/σ(I) obs: 2.3 / Num. unique all: 815 / % possible all: 98.5
Reflection
*PLUS
Lowest resolution: 25 Å
Reflection shell
*PLUS
Lowest resolution: 2.7 Å / % possible obs: 98.5 %

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Processing

Software
NameVersionClassificationNB
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: seqA-C

Resolution: 2.65→23.91 Å / Rfactor Rfree error: 0.008 / Occupancy max: 1 / Occupancy min: 1 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.278 1110 6.9 %random
Rwork0.248 ---
all-16285 --
obs-16158 99.2 %-
Solvent computationSolvent model: CNS bulk solvent model used / Bsol: 39.1035 Å2 / ksol: 0.300876 e/Å3
Displacement parametersBiso mean: 62.11 Å2
Baniso -1Baniso -2Baniso -3
1--0.74 Å20 Å20 Å2
2---0.74 Å20 Å2
3---1.47 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.44 Å0.41 Å
Luzzati d res low-3 Å
Luzzati sigma a0.58 Å0.38 Å
Refinement stepCycle: LAST / Resolution: 2.65→23.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1884 974 0 37 2895
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.008
X-RAY DIFFRACTIONx_angle_deg1.3
X-RAY DIFFRACTIONx_torsion_deg19.7
X-RAY DIFFRACTIONx_torsion_impr_deg1.27
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection Rfree% reflection Rfree (%)Rfactor RworkNum. reflection RworkRfactor Rfree error% reflection obs (%)
2.65-2.770.5211447.20.49818570.04398.9
2.77-2.920.4551276.40.4118680.0499.5
2.92-3.10.3371517.50.35618660.02799.5
3.1-3.340.3331276.30.2718780.0399.4
3.34-3.670.2811346.60.25118870.02499.8
3.67-4.20.2591527.50.22718680.02199.9
4.2-5.280.2221527.40.20418980.01899.6
5.28-23.910.24812360.21119260.02297.3
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2dna-rna_rep.paramdna-rna.top
X-RAY DIFFRACTION3water_rep.paramwater.top
Software
*PLUS
Name: CNS / Classification: refinement
Refinement
*PLUS
Lowest resolution: 25 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDType
X-RAY DIFFRACTIONc_bond_d
X-RAY DIFFRACTIONc_angle_deg

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