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- PDB-3rls: Crystal structure of yeast AF-9 homolog protein Yaf9 -

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Basic information

Entry
Database: PDB / ID: 3rls
TitleCrystal structure of yeast AF-9 homolog protein Yaf9
ComponentsProtein AF-9 homolog
KeywordsTRANSCRIPTION / YEATS domain / Histone
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 / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II ...Swr1 complex / NuA4 histone acetyltransferase complex / subtelomeric heterochromatin formation / histone binding / chromosome, telomeric region / chromatin remodeling / DNA repair / DNA-templated transcription / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / chromatin / 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 / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsChen, S.D. / Wu, L.J. / Liu, Y.F.
CitationJournal: To be Published
Title: Crystal structure of yeast AF-9 homolog protein yaf9
Authors: Liu, Y.F.
History
DepositionApr 20, 2011Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 25, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)40,4492
Polymers40,4492
Non-polymers00
Water7,062392
1
A: Protein AF-9 homolog


Theoretical massNumber of molelcules
Total (without water)20,2251
Polymers20,2251
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Protein AF-9 homolog


Theoretical massNumber of molelcules
Total (without water)20,2251
Polymers20,2251
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)32.643, 44.267, 62.158
Angle α, β, γ (deg.)71.78, 89.86, 83.31
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Protein AF-9 homolog / Yaf9


Mass: 20224.660 Da / Num. of mol.: 2 / Fragment: YEATS domain, residues in UNP 9-176
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: YAF9 / Production host: Escherichia coli (E. coli) / References: UniProt: P53930
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 392 / 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: 2.09 Å3/Da / Density % sol: 41.25 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 26% PEG 4000, 0.1M Tris-Cl, 0.1M Guanidine Hydrochloride, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Nov 23, 2009
RadiationScattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionHighest resolution: 1.7 Å / Num. obs: 33124

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Processing

Software
NameVersionClassification
PHASERphasing
REFMAC5.5.0072refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3FK3

3fk3


Resolution: 1.7→59 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.95 / SU B: 4.985 / SU ML: 0.072 / Cross valid method: THROUGHOUT / ESU R Free: 0.104 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20193 1730 5 %RANDOM
Rwork0.1578 ---
obs0.16001 33124 96.57 %-
all-33124 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 15.587 Å2
Baniso -1Baniso -2Baniso -3
1--0.65 Å20.9 Å2-0.05 Å2
2--0.61 Å20.48 Å2
3----0.47 Å2
Refinement stepCycle: LAST / Resolution: 1.7→59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2440 0 0 392 2832
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.0222551
X-RAY DIFFRACTIONr_bond_other_d0.0050.021776
X-RAY DIFFRACTIONr_angle_refined_deg1.511.9553474
X-RAY DIFFRACTIONr_angle_other_deg0.96534321
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6245300
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.42323.701127
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.70415419
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.9331514
X-RAY DIFFRACTIONr_chiral_restr0.1170.2368
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0212792
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02538
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.7881.51503
X-RAY DIFFRACTIONr_mcbond_other1.4521.5579
X-RAY DIFFRACTIONr_mcangle_it4.49522471
X-RAY DIFFRACTIONr_scbond_it5.88831048
X-RAY DIFFRACTIONr_scangle_it8.5134.5999
X-RAY DIFFRACTIONr_rigid_bond_restr3.65334327
X-RAY DIFFRACTIONr_sphericity_free20.5373392
X-RAY DIFFRACTIONr_sphericity_bonded3.5934244
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.258 122 -
Rwork0.199 2370 -
obs--94.86 %

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