[English] 日本語
Yorodumi
- PDB-5m1x: Crystal structure of S. cerevisiae Rfa1 N-OB domain mutant (K45E) -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5m1x
TitleCrystal structure of S. cerevisiae Rfa1 N-OB domain mutant (K45E)
ComponentsReplication factor A protein 1
KeywordsREPLICATION / OB fold
Function / homology
Function and homology information


heteroduplex formation / sporulation / DNA replication factor A complex / telomere maintenance via telomere lengthening / mitotic recombination / telomere maintenance via recombination / reciprocal meiotic recombination / DNA unwinding involved in DNA replication / DNA topological change / telomere maintenance via telomerase ...heteroduplex formation / sporulation / DNA replication factor A complex / telomere maintenance via telomere lengthening / mitotic recombination / telomere maintenance via recombination / reciprocal meiotic recombination / DNA unwinding involved in DNA replication / DNA topological change / telomere maintenance via telomerase / telomere maintenance / condensed nuclear chromosome / nucleotide-excision repair / double-strand break repair via homologous recombination / establishment of protein localization / single-stranded DNA binding / double-stranded DNA binding / sequence-specific DNA binding / DNA replication / chromosome, telomeric region / protein ubiquitination / DNA repair / mRNA binding / metal ion binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Replication factor A protein 1 / Replication factor-A protein 1, N-terminal / Replication protein A, OB domain / Replication protein A OB domain / : / Replication factor A, C-terminal / Replication factor-A C terminal domain / OB-fold nucleic acid binding domain, AA-tRNA synthetase-type / OB-fold nucleic acid binding domain / Nucleic acid-binding, OB-fold
Similarity search - Domain/homology
Replication factor A protein 1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae S288c (yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.8 Å
AuthorsSeeber, A. / Hegnauer, A.M. / Hustedt, N. / Deshpande, I. / Poli, J. / Eglinger, J. / Pasero, P. / Gut, H. / Shinohara, M. / Hopfner, K.P. ...Seeber, A. / Hegnauer, A.M. / Hustedt, N. / Deshpande, I. / Poli, J. / Eglinger, J. / Pasero, P. / Gut, H. / Shinohara, M. / Hopfner, K.P. / Shimada, K. / Gasser, S.M.
CitationJournal: Mol. Cell / Year: 2016
Title: RPA Mediates Recruitment of MRX to Forks and Double-Strand Breaks to Hold Sister Chromatids Together.
Authors: Seeber, A. / Hegnauer, A.M. / Hustedt, N. / Deshpande, I. / Poli, J. / Eglinger, J. / Pasero, P. / Gut, H. / Shinohara, M. / Hopfner, K.P. / Shimada, K. / Gasser, S.M.
History
DepositionOct 11, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 7, 2016Provider: repository / Type: Initial release
Revision 1.1Dec 14, 2016Group: Database references

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Replication factor A protein 1
B: Replication factor A protein 1
C: Replication factor A protein 1
D: Replication factor A protein 1


Theoretical massNumber of molelcules
Total (without water)62,4674
Polymers62,4674
Non-polymers00
Water7,332407
1
A: Replication factor A protein 1


Theoretical massNumber of molelcules
Total (without water)15,6171
Polymers15,6171
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Replication factor A protein 1


Theoretical massNumber of molelcules
Total (without water)15,6171
Polymers15,6171
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Replication factor A protein 1


Theoretical massNumber of molelcules
Total (without water)15,6171
Polymers15,6171
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Replication factor A protein 1


Theoretical massNumber of molelcules
Total (without water)15,6171
Polymers15,6171
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)29.620, 115.350, 69.030
Angle α, β, γ (deg.)90.00, 90.71, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein
Replication factor A protein 1 / RF-A protein 1 / DNA-binding protein BUF2 / Replication protein A 69 kDa DNA-binding subunit / ...RF-A protein 1 / DNA-binding protein BUF2 / Replication protein A 69 kDa DNA-binding subunit / Single-stranded DNA-binding protein


Mass: 15616.754 Da / Num. of mol.: 4 / Mutation: K45E
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae S288c (yeast) / Gene: RFA1, BUF2, RPA1, YAR007C, FUN3 / Plasmid: pOPINF / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P22336
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 407 / 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: 1.9 Å3/Da / Density % sol: 35.11 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 200 mM ammonium fluoride 20 % (w/v) PEG 3350

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Jun 5, 2014 / Details: Mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.8→44.26 Å / Num. obs: 80762 / % possible obs: 95.4 % / Observed criterion σ(I): -3 / Redundancy: 2.4 % / Biso Wilson estimate: 23.08 Å2 / CC1/2: 0.99 / Rsym value: 0.079 / Net I/σ(I): 8.02
Reflection shellResolution: 1.8→1.85 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.53 / Mean I/σ(I) obs: 1.74 / CC1/2: 0.68 / % possible all: 86.2

-
Processing

Software
NameVersionClassification
BUSTER2.11.5refinement
XDSdata reduction
XSCALEdata scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 1.8→44.26 Å / Cor.coef. Fo:Fc: 0.9467 / Cor.coef. Fo:Fc free: 0.9243 / SU R Cruickshank DPI: 0.134 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.135 / SU Rfree Blow DPI: 0.129 / SU Rfree Cruickshank DPI: 0.129
Details: Experimental details report unique reflections for unmerged Friedel pairs. Refinement was carried out on the same data with merged Friedel pairs. Automatic form factor correction at 0.97941 ...Details: Experimental details report unique reflections for unmerged Friedel pairs. Refinement was carried out on the same data with merged Friedel pairs. Automatic form factor correction at 0.97941 A was used for Se atoms in Buster.
RfactorNum. reflection% reflectionSelection details
Rfree0.2136 2086 5 %RANDOM
Rwork0.1644 ---
obs0.1669 41721 97.36 %-
Displacement parametersBiso mean: 31.72 Å2
Baniso -1Baniso -2Baniso -3
1-2.6259 Å20 Å2-0.994 Å2
2---8.2269 Å20 Å2
3---5.601 Å2
Refine analyzeLuzzati coordinate error obs: 0.209 Å
Refinement stepCycle: 1 / Resolution: 1.8→44.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4246 0 0 407 4653
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.014321HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.055833HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1579SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes135HARMONIC2
X-RAY DIFFRACTIONt_gen_planes626HARMONIC5
X-RAY DIFFRACTIONt_it4321HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.21
X-RAY DIFFRACTIONt_other_torsion16.96
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion564SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact5419SEMIHARMONIC4
LS refinement shellResolution: 1.8→1.85 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2387 141 4.97 %
Rwork0.1995 2695 -
all0.2015 2836 -
obs--97.36 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.83060.2422-0.44530.8045-0.50311.64750.0571-0.04170.27370.05120.0070.04950.03250.0265-0.0641-0.08480.0153-0.0142-0.02610.0161-0.000823.215285.16458.7282
22.0603-0.2892-0.74851.24820.25431.9899-0.0881-0.37140.17160.13230.16120.0230.03990.0914-0.0731-0.10140.0103-0.0209-0.0077-0.0705-0.025417.90432.215118.8834
31.319-0.31840.32031.3116-0.56052.1710.09350.127-0.1269-0.10690.06320.09880.0755-0.0336-0.1567-0.06320.0064-0.0515-0.0299-0.0056-0.024621.009362.323726.092
43.20430.73510.14211.8608-0.79542.08360.102-0.5447-0.24360.2188-0.1146-0.1583-0.13030.18790.0126-0.0956-0.0167-0.0603-0.02660.0467-0.075710.790358.9436-15.0668
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|* }
2X-RAY DIFFRACTION2{ B|* }
3X-RAY DIFFRACTION3{ C|* }
4X-RAY DIFFRACTION4{ D|* }

+
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://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