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- PDB-3fk3: Structure of the Yeats Domain, Yaf9 -

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Basic information

Entry
Database: PDB / ID: 3fk3
TitleStructure of the Yeats Domain, Yaf9
ComponentsProtein AF-9 homolog
KeywordsTRANSCRIPTION / beta-sandwich / Activator / Chromatin regulator / DNA damage / DNA repair / Nucleus / Transcription regulation
Function / homology
Function and homology information


Swr1 complex / NuA4 histone acetyltransferase complex / subtelomeric heterochromatin formation / histone binding / chromosome, telomeric region / chromatin remodeling / DNA repair / DNA-templated transcription / chromatin / regulation of DNA-templated transcription ...Swr1 complex / NuA4 histone acetyltransferase complex / subtelomeric heterochromatin formation / histone binding / chromosome, telomeric region / chromatin remodeling / DNA repair / DNA-templated transcription / chromatin / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / nucleus / cytoplasm
Similarity search - Function
YEATS domain / YEATS / YEATS superfamily / YEATS family / YEATS domain profile. / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Protein AF-9 homolog
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.3 Å
AuthorsWang, A.Y. / Schulze, J.M. / Skordalakes, E. / Berger, J.M. / Rine, J. / Kobor, M.S.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2009
Title: Asf1-like structure of the conserved Yaf9 YEATS domain and role in H2A.Z deposition and acetylation
Authors: Wang, A.Y. / Schulze, J.M. / Skordalakes, E. / Gin, J.W. / Berger, J.M. / Rine, J. / Kobor, M.S.
History
DepositionDec 15, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 27, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Mar 31, 2021Group: Data collection / Database references / Derived calculations
Category: reflns / struct_conn / struct_ref_seq_dif
Item: _reflns.pdbx_redundancy / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Protein AF-9 homolog
B: Protein AF-9 homolog
C: Protein AF-9 homolog


Theoretical massNumber of molelcules
Total (without water)57,0543
Polymers57,0543
Non-polymers00
Water3,729207
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4040 Å2
ΔGint-21 kcal/mol
Surface area23240 Å2
MethodPISA
2
A: Protein AF-9 homolog


Theoretical massNumber of molelcules
Total (without water)19,0181
Polymers19,0181
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
B: Protein AF-9 homolog


Theoretical massNumber of molelcules
Total (without water)19,0181
Polymers19,0181
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
C: Protein AF-9 homolog


Theoretical massNumber of molelcules
Total (without water)19,0181
Polymers19,0181
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)84.725, 84.725, 288.212
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522

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Components

#1: Protein Protein AF-9 homolog


Mass: 19017.979 Da / Num. of mol.: 3 / Fragment: YEATS domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: N1966, YAF9, YNL107W / Production host: Escherichia coli (E. coli) / References: UniProt: P53930
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 207 / 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: 2.62 Å3/Da / Density % sol: 53 %
Crystal growTemperature: 291 K / Method: microbatch / pH: 7.5
Details: 10% PEG 3350, 100 mM Na, Tartrate, 20% glycerol, pH 7.5, microbatch, temperature 291K

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.11587, 0.9795, 1.0199
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jun 15, 2004
RadiationMonochromator: KHOZU Double flat crystal / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.115871
20.97951
31.01991
ReflectionResolution: 2.3→20 Å / Num. obs: 24936 / % possible obs: 95.8 % / Observed criterion σ(F): 3 / Redundancy: 6.3 % / Rsym value: 0.063
Reflection shellResolution: 2.3→2.42 Å / Redundancy: 5 % / Rsym value: 0.368 / % possible all: 92.8

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
SOLVEphasing
REFMAC5.2.0019refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MAD / Resolution: 2.3→20 Å / Cor.coef. Fo:Fc: 0.924 / Cor.coef. Fo:Fc free: 0.899 / SU B: 13.958 / SU ML: 0.175 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.32 / ESU R Free: 0.237 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.25746 1323 5 %RANDOM
Rwork0.22217 ---
obs0.22394 24936 93.03 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 32.672 Å2
Baniso -1Baniso -2Baniso -3
1--1.87 Å2-0.93 Å20 Å2
2---1.87 Å20 Å2
3---2.8 Å2
Refinement stepCycle: LAST / Resolution: 2.3→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3471 0 0 207 3678
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0223576
X-RAY DIFFRACTIONr_angle_refined_deg0.9891.9474851
X-RAY DIFFRACTIONr_dihedral_angle_1_deg65414
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.36823.559177
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.94415597
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.7381521
X-RAY DIFFRACTIONr_chiral_restr0.0710.2516
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.022754
X-RAY DIFFRACTIONr_nbd_refined0.1840.21445
X-RAY DIFFRACTIONr_nbtor_refined0.3040.22398
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1050.2191
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.9460.259
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0770.211
X-RAY DIFFRACTIONr_mcbond_it0.331.52179
X-RAY DIFFRACTIONr_mcangle_it0.55123459
X-RAY DIFFRACTIONr_scbond_it0.52131599
X-RAY DIFFRACTIONr_scangle_it0.7994.51392
LS refinement shellResolution: 2.3→2.359 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.372 73 -
Rwork0.312 1138 -
obs--59.77 %
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)
15.1142-0.1658-0.87580.8389-0.06211.0136-0.02790.11860.1644-0.0999-0.0038-0.0351-0.05110.09950.0317-0.0142-0.01570.0607-0.07080.0034-0.107319.695651.453458.1328
21.7532-1.9735-0.15354.16460.27890.92390.03630.07360.011-0.0725-0.09410.1067-0.0802-0.14890.0579-0.06910.0110.0181-0.0680.0222-0.0741-19.960556.086562.7531
31.98222.0929-0.11174.3897-0.18350.8058-0.0720.0883-0.1569-0.2720.0572-0.14750.1207-0.03190.0148-0.02450.00090.0253-0.0753-0.0151-0.1224-3.913619.124760.7895
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A6 - 169
2X-RAY DIFFRACTION2B6 - 169
3X-RAY DIFFRACTION3C6 - 169

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