[English] 日本語
Yorodumi
- PDB-3t7i: Crystal structure of Se-Met Rtt107p (residues 820-1070) -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3t7i
TitleCrystal structure of Se-Met Rtt107p (residues 820-1070)
ComponentsRegulator of Ty1 transposition protein 107
KeywordsPROTEIN BINDING / BRCT / DNA repair / phospho-peptide
Function / homology
Function and homology information


regulation of DNA double-strand break processing / DNA double-strand break attachment to nuclear envelope / Cul8-RING ubiquitin ligase complex / retrotransposon silencing / regulation of DNA damage checkpoint / cell periphery / nucleosome assembly / double-strand break repair / nucleus
Similarity search - Function
Regulator of Ty1 transposition protein 107, BRCT domain / Regulator of Ty1 transposition protein 107 BRCT domain / Regulator of Ty1 transposition protein 107 BRCT domain / twin BRCT domain / BRCT domain / BRCA1 C Terminus (BRCT) domain / breast cancer carboxy-terminal domain / BRCT domain profile. / BRCT domain / BRCT domain superfamily ...Regulator of Ty1 transposition protein 107, BRCT domain / Regulator of Ty1 transposition protein 107 BRCT domain / Regulator of Ty1 transposition protein 107 BRCT domain / twin BRCT domain / BRCT domain / BRCA1 C Terminus (BRCT) domain / breast cancer carboxy-terminal domain / BRCT domain profile. / BRCT domain / BRCT domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Regulator of Ty1 transposition protein 107
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.3 Å
AuthorsLi, X. / Li, F. / Wu, J. / Shi, Y.
CitationJournal: J.Biol.Chem. / Year: 2012
Title: Structure of C-terminal Tandem BRCT Repeats of Rtt107 Protein Reveals Critical Role in Interaction with Phosphorylated Histone H2A during DNA Damage Repair
Authors: Li, X. / Liu, K. / Li, F. / Wang, J. / Huang, H. / Wu, J. / Shi, Y.
History
DepositionJul 30, 2011Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 15, 2012Provider: repository / Type: Initial release
Revision 1.1Apr 25, 2012Group: Database references
Revision 1.2Nov 8, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Regulator of Ty1 transposition protein 107
B: Regulator of Ty1 transposition protein 107


Theoretical massNumber of molelcules
Total (without water)59,1302
Polymers59,1302
Non-polymers00
Water2,036113
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Regulator of Ty1 transposition protein 107


Theoretical massNumber of molelcules
Total (without water)29,5651
Polymers29,5651
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
B: Regulator of Ty1 transposition protein 107


Theoretical massNumber of molelcules
Total (without water)29,5651
Polymers29,5651
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)59.236, 74.636, 129.080
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein Regulator of Ty1 transposition protein 107 / Rtt107


Mass: 29564.984 Da / Num. of mol.: 2 / Fragment: C-terminal domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: ATCC 204508 / S288c / Gene: RTT107 / Production host: Escherichia coli (E. coli) / References: UniProt: P38850
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 113 / 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: 2.41 Å3/Da / Density % sol: 49.02 % / Mosaicity: 0.699 °
Crystal growTemperature: 283 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 17.5%(w/v) MPEG2000, 0.1M HEPES, 0.2M NaCl, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 283K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9805, 0.9807, 0.9567
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Sep 13, 2010
RadiationMonochromator: plane grating / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.98051
20.98071
30.95671
ReflectionRedundancy: 12.2 % / Av σ(I) over netI: 53.31 / Number: 321261 / Rmerge(I) obs: 0.106 / Χ2: 3.77 / D res high: 2.3 Å / D res low: 50 Å / Num. obs: 26232 / % possible obs: 99.8
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
6.245097.810.0634.83911
4.956.2499.910.0734.1411.9
4.334.9599.610.0946.47411.9
3.934.3399.810.1118.10612.1
3.653.9399.810.1126.79412.3
3.443.6510010.1125.43412.4
3.263.4410010.1194.74112.5
3.123.2610010.1253.92812.5
33.1210010.1363.53912.5
2.9310010.1443.37912.5
2.812.910010.1563.1212.4
2.732.8110010.1752.77512.5
2.662.7310010.1862.6312.5
2.592.6610010.2032.5112.6
2.532.5910010.2212.57212.5
2.482.5310010.2442.29412.5
2.432.4810010.2632.11312.5
2.382.4310010.2832.0312.3
2.342.3899.710.3061.87412
2.32.3410010.3131.84211.7
ReflectionResolution: 2.3→50 Å / Num. all: 26285 / Num. obs: 26232 / % possible obs: 99.8 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 12.2 % / Rmerge(I) obs: 0.106 / Χ2: 3.765 / Net I/σ(I): 11.5
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.3-2.3411.70.31312791.8421100
2.34-2.38120.30612781.874199.7
2.38-2.4312.30.28312742.031100
2.43-2.4812.50.26313182.1131100
2.48-2.5312.50.24412782.2941100
2.53-2.5912.50.22113112.5721100
2.59-2.6612.60.20312722.511100
2.66-2.7312.50.18613092.631100
2.73-2.8112.50.17513082.7751100
2.81-2.912.40.15612843.121100
2.9-312.50.14412953.3791100
3-3.1212.50.13613243.5391100
3.12-3.2612.50.12512903.9281100
3.26-3.4412.50.11913214.7411100
3.44-3.6512.40.11213185.4341100
3.65-3.9312.30.11213256.794199.8
3.93-4.3312.10.11113208.106199.8
4.33-4.9511.90.09413396.474199.6
4.95-6.2411.90.07313634.14199.9
6.24-50110.06314264.839197.8

-
Phasing

PhasingMethod: MAD
Phasing set
ID
1
2
3
Phasing MADD res high: 2.09 Å / D res low: 1000 Å / FOM : 0.3 / Reflection: 34276
Phasing MAD set
Clust-IDExpt-IDSet-IDWavelength (Å)F double prime refinedF prime refined
3 wavelength110.98052.47-10.43
3 wavelength120.98071.39-8.04
3 wavelength130.95671.67-4.11
Phasing MAD set site
IDAtom type symbolB isoFract xFract yFract zOccupancy
1Se36.8860.2310.970.7361.416
2Se47.7040.1630.4860.0571.37
3Se48.8030.2380.470.8651.556
4Se49.240.1720.0110.0471.393
Phasing MAD shell
Resolution (Å)FOM Reflection
7.63-10000.671628
4.78-7.630.512874
3.73-4.780.363644
3.15-3.730.344311
2.78-3.150.344836
2.52-2.780.285334
2.32-2.520.195780
2.16-2.320.115869
Phasing dmFOM : 0.56 / FOM acentric: 0.56 / FOM centric: 0.58 / Reflection: 34224 / Reflection acentric: 30471 / Reflection centric: 3753
Phasing dm shell
Resolution (Å)FOM FOM acentricFOM centricReflectionReflection acentricReflection centric
3.7-60.910.920.8746653954711
3-3.70.810.820.7258185140678
2.6-30.620.630.5558325245587
2.2-2.60.390.40.33102839383900
2.1-2.20.210.210.260595594465

-
Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
SOLVE2.13phasing
RESOLVE2.15phasing
PHENIX1.6.1_357refinement
PDB_EXTRACT3.1data extraction
HKL-2000data collection
HKL-2000data reduction
RefinementMethod to determine structure: MAD / Resolution: 2.3→19.986 Å / Occupancy max: 1 / Occupancy min: 0 / SU ML: 0.33 / σ(F): 1.35 / Phase error: 26.23 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2481 1356 5.21 %RANDOM
Rwork0.2032 24656 --
obs0.2055 26012 99.66 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 42.976 Å2 / ksol: 0.277 e/Å3
Displacement parametersBiso max: 86.46 Å2 / Biso mean: 42.4719 Å2 / Biso min: 20 Å2
Baniso -1Baniso -2Baniso -3
1-1.7217 Å20 Å2-0 Å2
2--0.3152 Å20 Å2
3----2.0369 Å2
Refinement stepCycle: LAST / Resolution: 2.3→19.986 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3834 0 0 113 3947
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083898
X-RAY DIFFRACTIONf_angle_d1.0385244
X-RAY DIFFRACTIONf_chiral_restr0.072612
X-RAY DIFFRACTIONf_plane_restr0.004654
X-RAY DIFFRACTIONf_dihedral_angle_d13.7541480
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.3-2.38210.31651340.218324212555100
2.3821-2.47730.28351410.21124382579100
2.4773-2.58980.30251410.20824412582100
2.5898-2.7260.27221300.205324222552100
2.726-2.89640.30521240.215224532577100
2.8964-3.11920.27211390.22724612600100
3.1192-3.43170.27041350.204524562591100
3.4317-3.9250.22371360.186724912627100
3.925-4.93280.20111470.17282490263799
4.9328-19.98670.22261290.2032583271298

+
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