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- PDB-5gpl: Crystal structure of Ccp1 -

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Basic information

Entry
Database: PDB / ID: 5gpl
TitleCrystal structure of Ccp1
ComponentsPutative nucleosome assembly protein C36B7.08c
KeywordsCHAPERONE / Ccp1 dimer / nucleosome assembly protein
Function / homology
Function and homology information


CENP-A eviction from euchromatin / CENP-A containing chromatin / histone chaperone activity / chromosome, centromeric region / nucleosome assembly / histone binding / chromatin binding / chromatin / nucleoplasm / nucleus
Similarity search - Function
Nucleosome assembly protein (NAP) / NAP-like superfamily / Nucleosome assembly protein (NAP)
Similarity search - Domain/homology
Putative nucleosome assembly protein C36B7.08c
Similarity search - Component
Biological speciesSchizosaccharomyces pombe 972h- (yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsYin, F. / Gao, F. / Chen, Y.
CitationJournal: Mol.Cell / Year: 2016
Title: Ccp1 Homodimer Mediates Chromatin Integrity by Antagonizing CENP-A Loading
Authors: Dong, Q. / Yin, F.X. / Gao, F. / Shen, Y. / Zhang, F. / Li, Y. / He, H. / Gonzalez, M. / Yang, J. / Zhang, S. / Su, M. / Chen, Y.H. / Li, F.
History
DepositionAug 3, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 30, 2016Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_initial_refinement_model
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Putative nucleosome assembly protein C36B7.08c
B: Putative nucleosome assembly protein C36B7.08c


Theoretical massNumber of molelcules
Total (without water)64,7112
Polymers64,7112
Non-polymers00
Water4,648258
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2950 Å2
ΔGint-31 kcal/mol
Surface area22960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.662, 86.662, 158.771
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number91
Space group name H-MP4122
Components on special symmetry positions
IDModelComponents
11B-401-

HOH

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Components

#1: Protein Putative nucleosome assembly protein C36B7.08c / Ccp1


Mass: 32355.252 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Schizosaccharomyces pombe 972h- (yeast)
Strain: 972h- / Gene: SPBC36B7.08c
Production host: Schizosaccharomyces pombe expression vector pARG1B (others)
References: UniProt: Q9HGN2
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 258 / 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: 2.3 Å3/Da / Density % sol: 46.6 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 4
Details: 100mM sodiam manolate pH4.0 200mM NH4NO3 18% PEG 3,350 15% EG

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Type: MACSCIENCE / Wavelength: 0.97892 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Jun 1, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97892 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 36027 / % possible obs: 99.6 % / Redundancy: 14.4 % / Net I/σ(I): 23.8
Reflection shellResolution: 2.1→2.18 Å

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5GPK

5gpk


Resolution: 2.1→38.756 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.63
RfactorNum. reflection% reflection
Rfree0.2356 1742 4.84 %
Rwork0.1932 --
obs0.1952 35992 99.68 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.1→38.756 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3422 0 0 258 3680
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0033590
X-RAY DIFFRACTIONf_angle_d0.7314851
X-RAY DIFFRACTIONf_dihedral_angle_d14.6321384
X-RAY DIFFRACTIONf_chiral_restr0.03517
X-RAY DIFFRACTIONf_plane_restr0.003646
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1003-2.16210.27151510.22452787X-RAY DIFFRACTION99
2.1621-2.23190.25711450.21382802X-RAY DIFFRACTION99
2.2319-2.31170.2711400.20662771X-RAY DIFFRACTION99
2.3117-2.40420.22591510.20452822X-RAY DIFFRACTION100
2.4042-2.51360.23311550.20132785X-RAY DIFFRACTION100
2.5136-2.64610.25081280.21012821X-RAY DIFFRACTION100
2.6461-2.81180.25061480.21142846X-RAY DIFFRACTION100
2.8118-3.02890.26991410.21282835X-RAY DIFFRACTION100
3.0289-3.33350.22881480.20852880X-RAY DIFFRACTION100
3.3335-3.81550.23071480.19112875X-RAY DIFFRACTION100
3.8155-4.80570.19881250.16022953X-RAY DIFFRACTION100
4.8057-38.7630.22771620.17393073X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: 107.9225 Å / Origin y: 12.0658 Å / Origin z: 7.6996 Å
111213212223313233
T0.1537 Å2-0.0198 Å20.0004 Å2-0.1657 Å2-0.0164 Å2--0.1055 Å2
L1.1951 °2-1.0587 °2-0.1768 °2-1.3867 °20.1955 °2--0.0023 °2
S0.0434 Å °-0.023 Å °0.1071 Å °-0.0287 Å °-0.0061 Å °-0.1007 Å °-0.0439 Å °0.0501 Å °-0.0199 Å °
Refinement TLS groupSelection details: all

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