[English] 日本語
Yorodumi
- PDB-1lrr: CRYSTAL STRUCTURE OF E. COLI SEQA COMPLEXED WITH HEMIMETHYLATED DNA -

+
Open data


ID or keywords:

Loading...

-
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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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 %

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbjlvh1.pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more