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- PDB-5gpk: Crystal structure of Ccp1 mutant -

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Basic information

Entry
Database: PDB / ID: 5gpk
TitleCrystal structure of Ccp1 mutant
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 / SAD / Resolution: 2.103 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 13, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_entry_details / pdbx_modification_feature
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)65,1582
Polymers65,1582
Non-polymers00
Water6,359353
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3080 Å2
ΔGint-30 kcal/mol
Surface area22820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.814, 86.814, 158.776
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number91
Space group name H-MP4122

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Components

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


Mass: 32578.908 Da / Num. of mol.: 2 / Mutation: I117(MSE),L150(MSE)
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.: 353 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.31 Å3/Da / Density % sol: 46.73 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 4
Details: 100mM C3H2Na2O4, 200mM NH4NO3, 18% PEG 3350, 15% EG

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.97923 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: May 1, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97923 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 36042 / % possible obs: 99.74 % / Redundancy: 13.6 % / Net I/σ(I): 23.86
Reflection shellResolution: 2.1→2.18 Å

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Processing

Software
NameVersionClassification
PHENIX(1.10_2155: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.103→38.824 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.07 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2252 1799 5 %
Rwork0.1761 --
obs0.1786 35975 99.67 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.103→38.824 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3426 0 0 353 3779
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0093533
X-RAY DIFFRACTIONf_angle_d1.0334776
X-RAY DIFFRACTIONf_dihedral_angle_d19.1512166
X-RAY DIFFRACTIONf_chiral_restr0.06507
X-RAY DIFFRACTIONf_plane_restr0.006636
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1029-2.15970.23961210.20222569X-RAY DIFFRACTION99
2.1597-2.22330.22721380.19612568X-RAY DIFFRACTION100
2.2233-2.2950.24631310.18942577X-RAY DIFFRACTION100
2.295-2.3770.22751290.18462573X-RAY DIFFRACTION100
2.377-2.47220.2541470.18562592X-RAY DIFFRACTION100
2.4722-2.58470.25511400.18252606X-RAY DIFFRACTION100
2.5847-2.72090.25711470.18362595X-RAY DIFFRACTION100
2.7209-2.89130.22921170.17832634X-RAY DIFFRACTION100
2.8913-3.11450.25281430.17812623X-RAY DIFFRACTION100
3.1145-3.42770.20071370.16962646X-RAY DIFFRACTION100
3.4277-3.92330.17361560.16612656X-RAY DIFFRACTION100
3.9233-4.94140.21121400.14972694X-RAY DIFFRACTION100
4.9414-38.8310.25121530.18932843X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: 21.2849 Å / Origin y: 12.2113 Å / Origin z: 7.6194 Å
111213212223313233
T0.1501 Å2-0.0179 Å2-0.0098 Å2-0.1658 Å2-0.0239 Å2--0.1209 Å2
L1.1588 °2-1.0288 °2-0.2763 °2-1.1152 °20.171 °2---0.0523 °2
S0.007 Å °-0.0595 Å °0.1338 Å °0.0171 Å °0.0423 Å °-0.127 Å °-0.0285 Å °0.056 Å °-0.0172 Å °
Refinement TLS groupSelection details: all

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