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- PDB-6j0v: Crystal Structure of Yeast Rtt107 -

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Basic information

Entry
Database: PDB / ID: 6j0v
TitleCrystal Structure of Yeast Rtt107
ComponentsRegulator of Ty1 transposition protein 107
KeywordsPROTEIN BINDING / BRCT domain / mitosis / protein interaction
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 / BRCA1 C Terminus (BRCT) domain / breast cancer carboxy-terminal domain / BRCT domain profile. / BRCT domain / BRCT domain superfamily
Similarity search - Domain/homology
Regulator of Ty1 transposition protein 107
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.314 Å
AuthorsWan, B. / Wu, J. / Lei, M.
CitationJournal: Mol.Cell / Year: 2019
Title: Molecular Basis for Control of Diverse Genome Stability Factors by the Multi-BRCT Scaffold Rtt107.
Authors: Wan, B. / Wu, J. / Meng, X. / Lei, M. / Zhao, X.
History
DepositionDec 27, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 14, 2019Provider: repository / Type: Initial release
Revision 1.1Feb 26, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Mar 27, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)118,7202
Polymers118,7202
Non-polymers00
Water2,198122
1
A: Regulator of Ty1 transposition protein 107


Theoretical massNumber of molelcules
Total (without water)59,3601
Polymers59,3601
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Regulator of Ty1 transposition protein 107


Theoretical massNumber of molelcules
Total (without water)59,3601
Polymers59,3601
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)72.404, 98.905, 87.464
Angle α, β, γ (deg.)90.000, 108.970, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Regulator of Ty1 transposition protein 107 / Establishes silent chromatin protein 4


Mass: 59359.969 Da / Num. of mol.: 2 / Fragment: NTD domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: RTT107, ESC4, YHR154W / Plasmid: pGEX-6P1 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P38850
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 122 / 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: 2.49 Å3/Da / Density % sol: 50.69 % / Mosaicity: 0.12 °
Crystal growTemperature: 277 K / Method: evaporation / pH: 5.8
Details: 1.8M ammonium sulfate, 50mM sodium cacodylate pH 5.8, 5 mM magnesium acetate, 0.5mM spermine

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 0.97855 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Dec 30, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97855 Å / Relative weight: 1
ReflectionResolution: 2.31→98.9 Å / Num. obs: 49735 / % possible obs: 97.7 % / Redundancy: 3.7 % / Biso Wilson estimate: 52.55 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.07 / Rpim(I) all: 0.042 / Rrim(I) all: 0.082 / Net I/σ(I): 13.3 / Num. measured all: 182440
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.31-2.393.11.131313142360.3910.7581.368191
9.25-98.93.30.03224557380.9970.020.03838.388.1

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Processing

Software
NameVersionClassification
Aimless0.5.21data scaling
PHENIX1.13_2998refinement
PDB_EXTRACT3.24data extraction
Cootmodel building
SHELXDphasing
RefinementMethod to determine structure: SAD / Resolution: 2.314→49.452 Å / SU ML: 0.38 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 31.06 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2659 2482 5 %
Rwork0.2147 47187 -
obs0.2174 49669 97.48 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 197.43 Å2 / Biso mean: 71.7871 Å2 / Biso min: 23.44 Å2
Refinement stepCycle: final / Resolution: 2.314→49.452 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7503 0 0 122 7625
Biso mean---64.7 -
Num. residues----914
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 18

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.3137-2.35820.35241410.31452275241686
2.3582-2.40630.35351290.31352645277498
2.4063-2.45860.40291250.30232600272598
2.4586-2.51580.33751220.29352654277698
2.5158-2.57870.39121350.29512641277698
2.5787-2.64840.43451520.27912614276698
2.6484-2.72640.31041390.24562651279099
2.7264-2.81440.28751420.23972619276198
2.8144-2.91490.30341400.22992686282699
2.9149-3.03160.27631460.23652621276799
3.0316-3.16960.31611450.24032637278299
3.1696-3.33660.33351210.22762682280399
3.3366-3.54560.26461260.22292649277598
3.5456-3.81930.27421260.20732688281499
3.8193-4.20350.211400.19152644278498
4.2035-4.81130.22891440.16842637278198
4.8113-6.060.23581530.1872645279898
6.06-49.46380.22371560.19972599275595
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)
10.3888-0.1653-0.04592.22721.1171.6454-0.1159-0.01860.0725-0.07920.2929-0.1162-0.1017-0.02080.01580.18970.08350.03580.2971-0.00010.268141.92479.063112.986
21.76841.062-0.23161.89610.21410.7286-0.2160.20850.0701-0.13810.52540.40830.2417-0.32050.02430.4274-0.138-0.09190.41350.17140.389360.34680.075151.681
3-0.03020.2044-0.02290.3387-0.08870.2318-0.00770.0067-0.0833-0.01160.03470.0675-0.14390.0065-00.36660.05730.01790.3749-0.01830.354947.58176.507126.898
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 2:485 )A2 - 485
2X-RAY DIFFRACTION2( CHAIN B AND RESID 2:484 )B2 - 484
3X-RAY DIFFRACTION3( CHAIN A AND RESID 601:670 ) OR ( CHAIN B AND RESID 601:652 )A601 - 670
4X-RAY DIFFRACTION3( CHAIN A AND RESID 601:670 ) OR ( CHAIN B AND RESID 601:652 )B601 - 652

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