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- PDB-3t7i: Crystal structure of Se-Met Rtt107p (residues 820-1070) -

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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 / Cul8-RING ubiquitin ligase complex / DNA double-strand break attachment to nuclear envelope / transposable element silencing / regulation of DNA damage checkpoint / site of DNA damage / cell periphery / double-strand break repair / nucleosome assembly / chromatin binding / 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 ...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
Revision 1.3Nov 20, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_unobs_or_zero_occ_atoms / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details

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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)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

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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


Mass: 18.015 Da / Num. of mol.: 113 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.41 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

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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

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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

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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

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