[English] 日本語
Yorodumi
- PDB-4x01: S. pombe Ctp1 tetramerization domain -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4x01
TitleS. pombe Ctp1 tetramerization domain
ComponentsDNA binding ctp1
KeywordsDNA BINDING PROTEIN / Homologous Recombination / DNA Double-strand break repair / DNA Binding / Four-helix bundle
Function / homology
Function and homology information


double-strand/single-strand DNA junction binding / DNA-DNA tethering activity / stalled replication fork localization to nuclear periphery / endodeoxyribonuclease activator activity / meiotic DNA double-strand break processing / gene conversion at mating-type locus / flap-structured DNA binding / mitotic recombination-dependent replication fork processing / DNA end binding / Y-form DNA binding ...double-strand/single-strand DNA junction binding / DNA-DNA tethering activity / stalled replication fork localization to nuclear periphery / endodeoxyribonuclease activator activity / meiotic DNA double-strand break processing / gene conversion at mating-type locus / flap-structured DNA binding / mitotic recombination-dependent replication fork processing / DNA end binding / Y-form DNA binding / double-strand break repair involved in meiotic recombination / DNA double-strand break processing / bubble DNA binding / mitotic DNA replication checkpoint signaling / replication fork processing / double-strand break repair via homologous recombination / double-strand break repair via nonhomologous end joining / site of double-strand break / single-stranded DNA binding / double-stranded DNA binding / endonuclease activity / Hydrolases; Acting on ester bonds / identical protein binding / nucleus
Similarity search - Function
DNA endonuclease activator Ctp1, C-terminal / DNA endonuclease activator SAE2/CtIP C-terminus
Similarity search - Domain/homology
DNA endonuclease ctp1
Similarity search - Component
Biological speciesSchizosaccharomyces pombe (fission yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.201 Å
AuthorsAndres, S.N. / Williams, R.S.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS)1Z01ES102765 United States
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2015
Title: Tetrameric Ctp1 coordinates DNA binding and DNA bridging in DNA double-strand-break repair.
Authors: Andres, S.N. / Appel, C.D. / Westmoreland, J.W. / Williams, J.S. / Nguyen, Y. / Robertson, P.D. / Resnick, M.A. / Williams, R.S.
History
DepositionNov 20, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 14, 2015Provider: repository / Type: Initial release
Revision 1.1Jan 28, 2015Group: Database references
Revision 1.2Feb 18, 2015Group: Database references
Revision 1.3Aug 23, 2017Group: Data collection / Derived calculations ...Data collection / Derived calculations / Refinement description / Source and taxonomy / Structure summary
Category: diffrn_detector / entity_src_gen ...diffrn_detector / entity_src_gen / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_oper_list / software / struct_keywords
Item: _diffrn_detector.type / _entity_src_gen.pdbx_alt_source_flag ..._diffrn_detector.type / _entity_src_gen.pdbx_alt_source_flag / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_oper_list.symmetry_operation / _software.classification / _software.version / _struct_keywords.text
Revision 1.4Sep 6, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.6Sep 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: DNA binding ctp1
B: DNA binding ctp1
C: DNA binding ctp1
D: DNA binding ctp1
E: DNA binding ctp1
F: DNA binding ctp1
G: DNA binding ctp1
H: DNA binding ctp1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,61521
Polymers54,8088
Non-polymers80713
Water2,846158
1
A: DNA binding ctp1
B: DNA binding ctp1
C: DNA binding ctp1
D: DNA binding ctp1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,08715
Polymers27,4044
Non-polymers68311
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
E: DNA binding ctp1
F: DNA binding ctp1
G: DNA binding ctp1
H: DNA binding ctp1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,5286
Polymers27,4044
Non-polymers1242
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)49.071, 156.677, 48.927
Angle α, β, γ (deg.)90.00, 118.55, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein
DNA binding ctp1 / Double-strand break repair protein ctp1 / Meiotically up-regulated gene 38 protein / Nbs1- ...Double-strand break repair protein ctp1 / Meiotically up-regulated gene 38 protein / Nbs1-interacting protein 1 / Sporulation in the absence of SPO11 protein 2 homolog / SAE2


Mass: 6850.998 Da / Num. of mol.: 8 / Mutation: L51M
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Schizosaccharomyces pombe (fission yeast)
Strain: 972 / ATCC 24843 / Gene: ctp1, mug38, nip1, slr9, SPCC338.08 / Plasmid: pMCSG9 / Production host: Escherichia coli (E. coli)
References: UniProt: O74986, Hydrolases; Acting on ester bonds
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 158 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 3.01 Å3/Da / Density % sol: 59.2 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: Precipitant: 0.2M sodium acetate, 0.1M Tris pH 8.5 16% PEG 4000, with 0.4 uL of 0.1M barium chloride dihydrate additive. Cryoprotection in 25% ethylene glycol.

-
Data collection

DiffractionMean temperature: 105 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 3, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. obs: 32678 / % possible obs: 99.9 % / Redundancy: 3.8 % / Net I/σ(I): 20.7

-
Processing

Software
NameVersionClassification
PHENIX1.8.4_1496refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ID 1T6F

1t6f


Resolution: 2.201→40.676 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 28.96 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2455 1660 5.08 %
Rwork0.1979 --
obs0.2004 32678 99.68 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.201→40.676 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3214 0 52 158 3424
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0093285
X-RAY DIFFRACTIONf_angle_d0.9524368
X-RAY DIFFRACTIONf_dihedral_angle_d13.6451305
X-RAY DIFFRACTIONf_chiral_restr0.035505
X-RAY DIFFRACTIONf_plane_restr0.003527
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2013-2.26610.35851280.27722526X-RAY DIFFRACTION98
2.2661-2.33920.32411380.25382613X-RAY DIFFRACTION100
2.3392-2.42280.29291350.23042551X-RAY DIFFRACTION100
2.4228-2.51980.24951410.22342581X-RAY DIFFRACTION100
2.5198-2.63450.26651510.22662579X-RAY DIFFRACTION100
2.6345-2.77330.29321380.22722595X-RAY DIFFRACTION100
2.7733-2.9470.29861610.22662556X-RAY DIFFRACTION100
2.947-3.17450.27551260.22482597X-RAY DIFFRACTION100
3.1745-3.49380.24011420.2152621X-RAY DIFFRACTION100
3.4938-3.9990.21281390.18022571X-RAY DIFFRACTION100
3.999-5.03680.20631290.15952614X-RAY DIFFRACTION100
5.0368-40.68320.22721320.17862614X-RAY DIFFRACTION99

+
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