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- PDB-1roc: Crystal structure of the histone deposition protein Asf1 -

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Basic information

Entry
Database: PDB / ID: 1roc
TitleCrystal structure of the histone deposition protein Asf1
ComponentsAnti-silencing protein 1
KeywordsREPLICATION / CHAPERONE / beta-sandwich
Function / homology
Function and homology information


Formation of Senescence-Associated Heterochromatin Foci (SAHF) / : / H3 histone acetyltransferase complex / acetyltransferase activator activity / DNA replication-dependent chromatin assembly / nucleosome disassembly / : / silent mating-type cassette heterochromatin formation / subtelomeric heterochromatin formation / negative regulation of DNA damage checkpoint ...Formation of Senescence-Associated Heterochromatin Foci (SAHF) / : / H3 histone acetyltransferase complex / acetyltransferase activator activity / DNA replication-dependent chromatin assembly / nucleosome disassembly / : / silent mating-type cassette heterochromatin formation / subtelomeric heterochromatin formation / negative regulation of DNA damage checkpoint / regulation of DNA repair / positive regulation of transcription elongation by RNA polymerase II / regulation of protein phosphorylation / nucleosome assembly / chromatin organization / histone binding / regulation of gene expression / chromosome, telomeric region / regulation of transcription by RNA polymerase II / nucleus / cytosol
Similarity search - Function
Histone deposition protein Asf1 / Histone chaperone ASF1-like / Histone chaperone ASF1-like / Histone chaperone ASF1-like superfamily / ASF1 like histone chaperone / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
BROMIDE ION / Histone chaperone ASF1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.5 Å
AuthorsDaganzo, S.M. / Erzberger, J.P. / Lam, W.M. / Skordalakes, E. / Zhang, R. / Franco, A.A. / Brill, S.J. / Adams, P.D. / Berger, J.M. / Kaufman, P.D.
CitationJournal: Curr.Biol. / Year: 2003
Title: Structure and function of the conserved core of histone deposition protein Asf1.
Authors: Daganzo, S.M. / Erzberger, J.P. / Lam, W.M. / Skordalakes, E. / Zhang, R. / Franco, A.A. / Brill, S.J. / Adams, P.D. / Berger, J.M. / Kaufman, P.D.
History
DepositionDec 2, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 23, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Refinement description / Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Anti-silencing protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,21910
Polymers17,5001
Non-polymers7199
Water2,846158
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)94.395, 31.702, 53.625
Angle α, β, γ (deg.)90.00, 124.55, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Anti-silencing protein 1


Mass: 17499.730 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: ASF1, YJL115W, J0755 / Plasmid: pSV271 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 RIL / References: UniProt: P32447
#2: Chemical
ChemComp-BR / BROMIDE ION / Bromide


Mass: 79.904 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Br
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 158 / 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: 1.89 Å3/Da / Density % sol: 34.82 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: PEG 3350, sodium bromide, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal grow
*PLUS
Temperature: 18 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
110 mMHEPES-NaOH1droppH7.5
250 mM1dropNaCl
31 mMTCEP1drop
4100 mM1dropNH4F
5100 mM1dropNaBr
620 %PEG33501drop
80.85-1.0 M1reservoirNaBr
917 %PEG33501reservoir
7Asf1N1drop800nl
10Asf1N1reservoir900nl

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Data collection

DiffractionMean temperature: 200 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 0.956, 0.920
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 30, 2003
RadiationMonochromator: Double Crystal Si (111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.9561
20.921
ReflectionResolution: 1.4→50 Å / Num. all: 25672 / Num. obs: 23670 / % possible obs: 92.2 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 3.3 % / Rsym value: 0.06 / Net I/σ(I): 18.8
Reflection shellResolution: 1.4→1.46 Å / Redundancy: 1.5 % / Mean I/σ(I) obs: 1.9 / Rsym value: 0.34 / % possible all: 48

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
HKL-2000data reduction
SCALEPACKdata scaling
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 1.5→30 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.926 / SU B: 1.685 / SU ML: 0.063 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 2.6 / ESU R: 0.095 / ESU R Free: 0.1 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.2465 1085 5.2 %RANDOM
Rwork0.19766 ---
all0.2001 20158 --
obs0.20012 19972 99.08 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 18.847 Å2
Baniso -1Baniso -2Baniso -3
1-0.72 Å20 Å20.32 Å2
2---0.23 Å20 Å2
3----0.13 Å2
Refinement stepCycle: LAST / Resolution: 1.5→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1235 0 9 158 1402
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0211264
X-RAY DIFFRACTIONr_angle_refined_deg1.0941.9641724
X-RAY DIFFRACTIONr_dihedral_angle_1_deg18.9135154
X-RAY DIFFRACTIONr_chiral_restr0.0810.2197
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02966
X-RAY DIFFRACTIONr_nbd_refined0.2180.2528
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1740.2116
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2140.287
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1520.224
X-RAY DIFFRACTIONr_mcbond_it0.6751.5777
X-RAY DIFFRACTIONr_mcangle_it1.30721272
X-RAY DIFFRACTIONr_scbond_it2.1123487
X-RAY DIFFRACTIONr_scangle_it3.5134.5452
LS refinement shellResolution: 1.5→1.539 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.333 85
Rwork0.271 1343
Refinement TLS params.Method: refined / Origin x: 61.9243 Å / Origin y: 9.4668 Å / Origin z: 7.3717 Å
111213212223313233
T0.0091 Å20.0051 Å20 Å2-0.0058 Å20.0069 Å2--0.0161 Å2
L0.2775 °20.0552 °2-0.1345 °2-0.373 °20.1358 °2--0.6386 °2
S0.0164 Å °0.0281 Å °0.0133 Å °0.0036 Å °0.0154 Å °-0.0208 Å °-0.0187 Å °-0.0194 Å °-0.0318 Å °
Refinement
*PLUS
Highest resolution: 1.5 Å / Lowest resolution: 30 Å / Num. reflection Rfree: 1082 / Rfactor Rwork: 0.1977
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.009
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg1.094

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