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- PDB-3gyp: Rtt106p -

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Basic information

Entry
Database: PDB / ID: 3gyp
TitleRtt106p
ComponentsHistone chaperone RTT106
KeywordsCHAPERONE / histone chaperone / Chromosomal protein / Nucleus / Phosphoprotein / Transcription / Transcription regulation / Transposition
Function / homology
Function and homology information


transposition / DNA replication-dependent chromatin assembly / heterochromatin formation / nucleosome binding / transcription elongation by RNA polymerase II / chromatin organization / chromosome / histone binding / double-stranded DNA binding / negative regulation of transcription by RNA polymerase II ...transposition / DNA replication-dependent chromatin assembly / heterochromatin formation / nucleosome binding / transcription elongation by RNA polymerase II / chromatin organization / chromosome / histone binding / double-stranded DNA binding / negative regulation of transcription by RNA polymerase II / identical protein binding / nucleus
Similarity search - Function
PH-domain like - #120 / Rtt106, pleckstrin homology domain / Histone chaperone Rtt106, N-terminal domain / Histone chaperone Rtt106, N-terminal domain superfamily / Histone chaperone Rtt106 N-terminal domain / Pleckstrin homology domain / Histone chaperone RTT106/FACT complex subunit SPT16-like, middle domain / Histone chaperone Rttp106-like, middle domain / Histone chaperone Rttp106-like / Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) ...PH-domain like - #120 / Rtt106, pleckstrin homology domain / Histone chaperone Rtt106, N-terminal domain / Histone chaperone Rtt106, N-terminal domain superfamily / Histone chaperone Rtt106 N-terminal domain / Pleckstrin homology domain / Histone chaperone RTT106/FACT complex subunit SPT16-like, middle domain / Histone chaperone Rttp106-like, middle domain / Histone chaperone Rttp106-like / Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) / PH-domain like / PH-like domain superfamily / Roll / Mainly Beta
Similarity search - Domain/homology
BETA-MERCAPTOETHANOL / Histone chaperone RTT106
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.406 Å
AuthorsLiu, Y. / Huang, H. / Shi, Y. / Teng, M.
CitationJournal: J.Biol.Chem. / Year: 2010
Title: Structural analysis of Rtt106p reveals a DNA-binding role required for heterochromatin silencing
Authors: Liu, Y. / Huang, H. / Zhou, B.O. / Wang, S.S. / Hu, Y. / Li, X. / Liu, J. / Zang, J. / Niu, L. / Wu, J. / Zhou, J.Q. / Teng, M. / Shi, Y.
History
DepositionApr 4, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 8, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Refinement description / Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: 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 10, 2021Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Histone chaperone RTT106
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,9213
Polymers29,8071
Non-polymers1142
Water95553
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)46.417, 54.006, 109.510
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 Histone chaperone RTT106 / Regulator of Ty1 transposition protein 106


Mass: 29807.162 Da / Num. of mol.: 1 / Fragment: residues in UNP 65-320
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: RTT106 / Production host: Escherichia coli (E. coli) / References: UniProt: P40161
#2: Chemical ChemComp-BME / BETA-MERCAPTOETHANOL


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 53 / 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: 2.3 Å3/Da / Density % sol: 46.52 % / Mosaicity: 0.51 °
Crystal growTemperature: 285 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 18%w/v PEG 4000, 100mM NaAc, 1%v/v jeffamine ED-2001, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 285K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BSRF / Beamline: 3W1A / Wavelength: 1 Å
DetectorDate: Jan 13, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.4→20 Å / Num. obs: 10353 / % possible obs: 92.6 % / Redundancy: 6 % / Rmerge(I) obs: 0.075 / Χ2: 0.78 / Net I/σ(I): 20.117
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.4-2.512.80.2578210.597159.9
2.51-2.643.80.24811300.584182.4
2.64-2.815.50.21413240.595197.2
2.81-3.026.70.15613650.6321100
3.02-3.327.10.10114030.7631100
3.32-3.87.10.07613890.8371100
3.8-4.7870.06314200.931100
4.78-206.60.05815010.964199.9

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACT3.006data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.406→19.81 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.905 / WRfactor Rfree: 0.264 / WRfactor Rwork: 0.211 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.775 / SU B: 20.169 / SU ML: 0.234 / SU R Cruickshank DPI: 0.455 / SU Rfree: 0.295 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.455 / ESU R Free: 0.295 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.274 490 4.8 %RANDOM
Rwork0.218 ---
obs0.221 10311 92.11 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 75.95 Å2 / Biso mean: 42.323 Å2 / Biso min: 24.92 Å2
Baniso -1Baniso -2Baniso -3
1--1.94 Å20 Å20 Å2
2--0.48 Å20 Å2
3---1.45 Å2
Refinement stepCycle: LAST / Resolution: 2.406→19.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1743 0 5 53 1801
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0221781
X-RAY DIFFRACTIONr_angle_refined_deg1.5931.972415
X-RAY DIFFRACTIONr_dihedral_angle_1_deg10.9965223
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.9525.13574
X-RAY DIFFRACTIONr_dihedral_angle_3_deg22.12515296
X-RAY DIFFRACTIONr_dihedral_angle_4_deg25.949154
X-RAY DIFFRACTIONr_chiral_restr0.1130.2285
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021318
X-RAY DIFFRACTIONr_nbd_refined0.2230.2721
X-RAY DIFFRACTIONr_nbtor_refined0.3050.21207
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1290.269
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2560.226
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2290.21
X-RAY DIFFRACTIONr_mcbond_it0.531.51143
X-RAY DIFFRACTIONr_mcangle_it0.79321821
X-RAY DIFFRACTIONr_scbond_it1.4173703
X-RAY DIFFRACTIONr_scangle_it2.0754.5594
LS refinement shellResolution: 2.406→2.468 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.494 16 -
Rwork0.289 399 -
all-415 -
obs--50.92 %
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)
174.0218-40.363730.316243.7667-24.859422.80810.93580.7887-1.413-3.1365-0.38252.70891.298-1.1665-0.5532-0.0127-0.1173-0.11390.1424-0.0516-0.1065-30.0954-0.08021.886
219.22572.60963.04626.2256-0.13696.6405-0.28180.00550.8968-0.32650.1670.1285-0.0247-0.2230.1148-0.07780.0114-0.0023-0.1778-0.0251-0.3078-17.1435.57965.5207
317.5994-5.7835-5.4813.8981-0.48244.3175-0.25590.70240.0517-0.36050.42760.1429-0.0806-0.2757-0.1717-0.0444-0.0136-0.0669-0.0527-0.0843-0.2177-20.49321.87285.5022
413.03630.1465-1.47025.25550.58327.3461-0.14530.5273-0.5906-0.17620.160.40770.6914-0.7929-0.0147-0.1214-0.0109-0.1202-0.15-0.0280.0273-23.7461-2.11718.1626
514.26375.9691-0.881910.1582-4.40742.1834-0.39790.4544-1.3255-1.07070.1467-0.40280.4481-0.12550.2512-0.10030.0039-0.0834-0.1136-0.05330.1369-19.078-3.75668.2063
65.50371.09332.99795.89580.33732.02850.4168-0.91360.0020.1467-0.42480.3920.1040.02240.008-0.10860.023-0.0496-0.02140.0183-0.1637-14.475.532819.3097
78.03975.54951.371918.6318-4.33345.2162-0.2871-0.09680.4826-0.5092-0.0158-0.2552-0.16910.19710.3028-0.21560.04070.0036-0.073-0.0126-0.1685-9.52078.702813.6954
84.22331.05961.18392.28452.14252.0190.08110.02460.2256-0.5008-0.2753-0.0831-0.0179-0.15210.1942-0.14860.0093-0.0907-0.0144-0.0197-0.1831-16.31268.01829.1567
94.02943.2811-2.487914.9243-4.90146.59760.0082-0.21770.8185-0.3303-0.10121.6029-0.4392-0.46870.093-0.13970.1088-0.1257-0.0038-0.14860.137-22.930315.570713.6606
1021.3884-4.4405-4.14496.73432.65316.4424-0.0892-0.11380.10160.4736-0.1739-0.213-0.31480.2080.2631-0.1205-0.0301-0.0907-0.1553-0.0619-0.09522.266412.79322.3668
1111.0681-2.60340.1415.81171.095.73020.11570.12750.52550.2024-0.0899-0.1805-0.17630.3991-0.0258-0.1752-0.0073-0.0895-0.1358-0.0799-0.10120.798710.284620.9932
1210.37642.88253.09812.93160.704411.9656-0.04530.255-0.65370.3370.25530.1450.8425-0.3241-0.2099-0.12530.0309-0.0865-0.166-0.0369-0.1149-3.19086.344421.4444
135.70910.5591-2.33956.13051.318139.74580.138-0.6783-0.79090.2155-0.23170.4841-0.35550.47380.0937-0.08580.092-0.1064-0.2075-0.0240.0386-2.43981.606725.6969
1455.292641.8427-9.173438.5651-14.10948.96650.6334-1.9269-0.33230.1052-1.5563-1.03511.58350.80630.92290.2338-0.0302-0.14590.1089-0.20640.01148.93197.346334.0519
154.63695.1069-4.18619.1086-9.45459.75890.2547-0.3483-0.25470.7571-0.3573-1.2243-0.40221.17040.1026-0.0163-0.0915-0.070.0808-0.1547-0.048510.12519.335428.9664
163.31070.0194-2.542825.8721-12.96459.23140.2287-0.28910.08520.2661-0.4490.1220.021.02060.2202-0.0824-0.0066-0.0887-0.0206-0.08-0.1027.46124.513326.1987
1720.461110.48778.226312.21896.91226.9950.0165-2.26070.53030.2675-0.7205-0.7238-0.8585-0.41250.7039-0.08130.0075-0.10170.0973-0.2259-0.13561.590915.127833.2818
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A7 - 11
2X-RAY DIFFRACTION2A12 - 26
3X-RAY DIFFRACTION3A27 - 38
4X-RAY DIFFRACTION4A39 - 50
5X-RAY DIFFRACTION5A51 - 60
6X-RAY DIFFRACTION6A61 - 72
7X-RAY DIFFRACTION7A73 - 88
8X-RAY DIFFRACTION8A89 - 115
9X-RAY DIFFRACTION9A116 - 141
10X-RAY DIFFRACTION10A159 - 168
11X-RAY DIFFRACTION11A169 - 178
12X-RAY DIFFRACTION12A179 - 186
13X-RAY DIFFRACTION13A187 - 197
14X-RAY DIFFRACTION14A198 - 204
15X-RAY DIFFRACTION15A205 - 217
16X-RAY DIFFRACTION16A218 - 228
17X-RAY DIFFRACTION17A229 - 242

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