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- PDB-2cu9: Crystal structure of Histone chaperone cia1 -

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Basic information

Entry
Database: PDB / ID: 2cu9
TitleCrystal structure of Histone chaperone cia1
ComponentsHistone chaperone cia1
KeywordsCHAPERONE / immunoglobulin fold / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homology
Function and homology information


H3-H4 histone complex chaperone activity / histone chaperone activity / DNA replication-dependent chromatin assembly / nucleosome disassembly / nucleosome assembly / chromatin organization / histone binding / chromatin remodeling / chromatin / nucleus
Similarity search - Function
Histone chaperone ASF1-like / Histone deposition protein Asf1 / Histone chaperone ASF1-like / Histone chaperone ASF1-like superfamily / ASF1 like histone chaperone / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Histone chaperone cia1
Similarity search - Component
Biological speciesSchizosaccharomyces pombe (fission yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsPadmanabhan, B. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: J.Biol.Chem. / Year: 2008
Title: Crystal Structures of Fission Yeast Histone Chaperone Asf1 Complexed with the Hip1 B-domain or the Cac2 C Terminus
Authors: Malay, A.D. / Umehara, T. / Matsubara-Malay, K. / Padmanabhan, B. / Yokoyama, S.
History
DepositionMay 25, 2005Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 29, 2006Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 25, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: Histone chaperone cia1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,4682
Polymers18,3481
Non-polymers1201
Water4,468248
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)78.623, 41.297, 67.211
Angle α, β, γ (deg.)90.00, 115.65, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Histone chaperone cia1 / spCia1


Mass: 18347.934 Da / Num. of mol.: 1 / Fragment: N-terminal region 1-161
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Schizosaccharomyces pombe (fission yeast)
Plasmid: pET15b / Production host: Escherichia coli (E. coli) / References: UniProt: O74515
#2: Chemical ChemComp-PG0 / 2-(2-METHOXYETHOXY)ETHANOL / PEG 6000 / 2-(2-Methoxyethoxy)ethanol


Mass: 120.147 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H12O3 / Comment: inhibitor, precipitant*YM
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 248 / 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: 2.68 Å3/Da / Density % sol: 58 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 8
Details: PEG 6000, Ammonium Sulfate, pH 8.0, VAPOR DIFFUSION, temperature 293K

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B1 / Wavelength: 1 Å
DetectorType: RIGAKU JUPITER 210 / Detector: CCD / Date: Sep 24, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 17836 / % possible obs: 97.7 % / Observed criterion σ(I): -3 / Redundancy: 3.5 % / Rmerge(I) obs: 0.082
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.175 / Num. unique all: 1610 / % possible all: 87.4

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
HKL-2000data reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1WG3

1wg3


Resolution: 1.8→20 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.94 / SU B: 2.947 / SU ML: 0.092 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.133 / ESU R Free: 0.133 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.23891 911 5.1 %RANDOM
Rwork0.19136 ---
obs0.19387 16878 97.67 %-
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: 33.102 Å2
Baniso -1Baniso -2Baniso -3
1--0.16 Å20 Å21.12 Å2
2--0.06 Å20 Å2
3---1.07 Å2
Refinement stepCycle: LAST / Resolution: 1.8→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1274 0 8 248 1530
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0221307
X-RAY DIFFRACTIONr_angle_refined_deg1.3661.9711778
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7875160
X-RAY DIFFRACTIONr_chiral_restr0.0940.2207
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02975
X-RAY DIFFRACTIONr_nbd_refined0.2110.2571
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1380.2150
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2270.235
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1410.212
X-RAY DIFFRACTIONr_mcbond_it0.9931.5807
X-RAY DIFFRACTIONr_mcangle_it1.80221317
X-RAY DIFFRACTIONr_scbond_it2.3323500
X-RAY DIFFRACTIONr_scangle_it3.9054.5461
LS refinement shellResolution: 1.8→1.846 Å / Total num. of bins used: 20
RfactorNum. reflection
Rfree0.259 56
Rwork0.21 1059
obs-1059

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