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- PDB-3tvv: Structure of the tandem PH domains of Rtt106 (residues 68-315) -

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Basic information

Entry
Database: PDB / ID: 3tvv
TitleStructure of the tandem PH domains of Rtt106 (residues 68-315)
ComponentsHistone chaperone RTT106
KeywordsCHAPERONE / tandem pleckstrin-homology domains / chromosomal protein / nucleus / phosphoprotein / transcription / transcription regulation
Function / homology
Function and homology information


transposition / DNA replication-dependent chromatin assembly / nucleosome binding / heterochromatin formation / transcription elongation by RNA polymerase II / chromosome / chromatin organization / histone binding / double-stranded DNA binding / negative regulation of transcription by RNA polymerase II ...transposition / DNA replication-dependent chromatin assembly / nucleosome binding / heterochromatin formation / transcription elongation by RNA polymerase II / chromosome / chromatin organization / 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
Histone chaperone RTT106
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.589 Å
AuthorsSu, D. / Thompson, J.R. / Mer, G.
CitationJournal: Nature / Year: 2012
Title: Structural basis for recognition of H3K56-acetylated histone H3-H4 by the chaperone Rtt106.
Authors: Su, D. / Hu, Q. / Li, Q. / Thompson, J.R. / Cui, G. / Fazly, A. / Davies, B.A. / Botuyan, M.V. / Zhang, Z. / Mer, G.
History
DepositionSep 20, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 1, 2012Provider: repository / Type: Initial release
Revision 1.1Feb 22, 2012Group: Database references
Revision 1.2Mar 7, 2012Group: Database references
Revision 1.3Jul 17, 2019Group: Data collection / Derived calculations / Refinement description
Category: software / struct_conn
Item: _software.classification / _software.name ..._software.classification / _software.name / _software.version / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4Sep 13, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.5Dec 6, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Histone chaperone RTT106
B: Histone chaperone RTT106


Theoretical massNumber of molelcules
Total (without water)58,2632
Polymers58,2632
Non-polymers00
Water2,648147
1
A: Histone chaperone RTT106


Theoretical massNumber of molelcules
Total (without water)29,1311
Polymers29,1311
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Histone chaperone RTT106


Theoretical massNumber of molelcules
Total (without water)29,1311
Polymers29,1311
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)70.660, 60.640, 77.170
Angle α, β, γ (deg.)90.00, 102.49, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Histone chaperone RTT106 / Regulator of Ty1 transposition protein 106


Mass: 29131.434 Da / Num. of mol.: 2 / Fragment: UNP residues 68-315
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: ATCC 204508 / S288c / Gene: N1346, RTT106, YNL206C / Plasmid: PTEV / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P40161
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 147 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsMUTATION N171K IS A NATURAL VARIANT.

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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: 2.77 Å3/Da / Density % sol: 55.6 %
Crystal growTemperature: 288 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 8% v/v tacsimate, 20% PEG3350, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 288K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9793
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 2, 2009
RadiationMonochromator: double-crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.563→34.3 Å / Num. all: 20711 / Num. obs: 19166 / % possible obs: 93.9 % / Redundancy: 3.3 % / Rmerge(I) obs: 0.098 / Net I/σ(I): 18.1
Reflection shellResolution: 2.563→2.66 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.45 / Mean I/σ(I) obs: 2.1 / % possible all: 66.3

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Processing

Software
NameVersionClassification
PHENIXdev_886refinement
PHASERphasing
REFMAC5.5.0070refinement
HKL-3000data reduction
HKL-3000data scaling
HKL-3000data collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3FSS

3fss


Resolution: 2.589→31.307 Å / Cor.coef. Fo:Fc: 0.927 / Cor.coef. Fo:Fc free: 0.855 / SU ML: 0.39 / σ(F): 1.34 / Phase error: 35.03 / Stereochemistry target values: ML / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflection
Rfree0.2942 862 5.13 %
Rwork0.2379 --
obs0.2408 16799 83.56 %
Solvent computationShrinkage radii: 0.73 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 29.309 Å2 / ksol: 0.278 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--13.8777 Å20 Å23.6676 Å2
2--13.4915 Å20 Å2
3---0.3861 Å2
Refinement stepCycle: LAST / Resolution: 2.589→31.307 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3791 0 0 147 3938
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0023960
X-RAY DIFFRACTIONf_angle_d0.6485357
X-RAY DIFFRACTIONf_dihedral_angle_d11.3251532
X-RAY DIFFRACTIONf_chiral_restr0.04610
X-RAY DIFFRACTIONf_plane_restr0.003678
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.589-2.75070.4974450.3868863X-RAY DIFFRACTION27
2.7507-2.96290.41261330.32792481X-RAY DIFFRACTION79
2.9629-3.26080.35891810.2933123X-RAY DIFFRACTION99
3.2608-3.7320.28731410.24823200X-RAY DIFFRACTION100
3.732-4.69930.25111850.19233117X-RAY DIFFRACTION99
4.6993-31.30940.28721770.22923153X-RAY DIFFRACTION97
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)
18.07854.07930.31468.7747-1.654.43350.3936-0.92020.81471.1888-0.4152-0.0012-0.53880.35750.00260.5596-0.0389-0.01190.3818-0.09940.535955.82275.386445.4532
22.38761.88580.99649.86472.76864.45120.10540.13330.30810.0775-0.09250.08210.10390.2238-0.01380.34230.00640.04230.3408-0.00640.369244.9861-7.710533.9718
39.555-5.4059-2.04442.00093.2158.63060.11740.6189-0.9113-1.4529-0.9452.60860.5168-0.64150.84280.81560.0031-0.14790.6786-0.16760.579219.2425-2.35741.8
44.2469-2.0555-0.09117.25491.18323.07470.13410.9919-0.3706-0.6177-0.35470.09720.8775-0.1460.21280.6942-0.0240.01770.5521-0.11310.335728.0825-2.42361.3352
52.0121-2.7109-6.22659.83221.36244.9178-0.04990.99420.5316-0.67370.2344-0.04750.6836-0.4331-0.19050.7442-0.1057-0.16340.6656-0.07630.490928.31978.00666.5041
66.1348-2.7767-1.67536.1296-0.61665.7999-0.2029-0.3346-0.72870.35910.21440.91250.7509-0.1374-0.01730.8897-0.0459-0.14860.28980.02540.522219.627-1.213215.6081
77.25542.08820.03188.10151.79478.25610.13620.29460.3-0.5335-0.2260.4477-0.28050.3280.06140.3907-0.00720.00070.2921-0.01640.235533.28222.724115.614
82.0085-9.0472-7.21172.01734.04928.4044-0.2487-1.34840.60990.99530.3551-0.9074-0.05811.196-0.09541.04-0.1841-0.17630.5473-0.01680.897242.198216.655725.331
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resseq 0:130)
2X-RAY DIFFRACTION2chain 'A' and (resseq 131:310)
3X-RAY DIFFRACTION3chain 'B' and (resseq -1:95)
4X-RAY DIFFRACTION4chain 'B' and (resseq 96:130)
5X-RAY DIFFRACTION5chain 'B' and (resseq 131:153)
6X-RAY DIFFRACTION6chain 'B' and (resseq 154:219)
7X-RAY DIFFRACTION7chain 'B' and (resseq 220:287)
8X-RAY DIFFRACTION8chain 'B' and (resseq 288:311)

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