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- PDB-5z07: Crystal structure of centromere protein Cenp-I -

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Basic information

Entry
Database: PDB / ID: 5z07
TitleCrystal structure of centromere protein Cenp-I
ComponentsCenp-I
KeywordsCELL CYCLE / kinetochore / centromere
Function / homologyCentromere protein I / Mis6 / centromere complex assembly / kinetochore / nucleus / Uncharacterized protein
Function and homology information
Biological speciesChaetomium thermophilum (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.298 Å
AuthorsTian, W. / Hu, L.Q. / He, X.
Funding support China, 3items
OrganizationGrant numberCountry
National Natural Science Foundation of China31500605 China
National Natural Science Foundation of China31500629 China
National Natural Science Foundation of China31470763 China
CitationJournal: Nucleic Acids Res. / Year: 2019
Title: Structural analysis of fungal CENP-H/I/K homologs reveals a conserved assembly mechanism underlying proper chromosome alignment.
Authors: Hu, L. / Huang, H. / Hei, M. / Yang, Y. / Li, S. / Liu, Y. / Dou, Z. / Wu, M. / Li, J. / Wang, G.Z. / Yao, X. / Liu, H. / He, X. / Tian, W.
History
DepositionDec 18, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 31, 2018Provider: repository / Type: Initial release
Revision 1.1May 15, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 16, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _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: Cenp-I


Theoretical massNumber of molelcules
Total (without water)25,8861
Polymers25,8861
Non-polymers00
Water1,62190
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area10930 Å2
Unit cell
Length a, b, c (Å)59.671, 59.671, 145.971
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11A-771-

HOH

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Components

#1: Protein Cenp-I


Mass: 25885.646 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719) (fungus)
Strain: DSM 1495 / CBS 144.50 / IMI 039719 / Gene: CTHT_0061880 / Production host: Escherichia coli (E. coli) / References: UniProt: G0SFF7
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 90 / 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: 2.51 Å3/Da / Density % sol: 50.99 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: PEG4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NFPSS / Beamline: BL18U / Wavelength: 0.987 Å
DetectorType: RAYONIX MX225-HS / Detector: CCD / Date: Dec 8, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 2.298→50 Å / Num. obs: 12379 / % possible obs: 99.7 % / Redundancy: 4.5 % / Net I/σ(I): 21.4

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Processing

Software
NameVersionClassification
PHENIX(dev_2463)refinement
AutoSoldata reduction
HKL-3000data scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.298→46.197 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 23.34
RfactorNum. reflection% reflection
Rfree0.2277 1238 10 %
Rwork0.1739 --
obs0.1793 12379 99.75 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.298→46.197 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1700 0 0 90 1790
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071737
X-RAY DIFFRACTIONf_angle_d0.9612362
X-RAY DIFFRACTIONf_dihedral_angle_d7.645639
X-RAY DIFFRACTIONf_chiral_restr0.053278
X-RAY DIFFRACTIONf_plane_restr0.007300
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2983-2.39030.28671340.21321202X-RAY DIFFRACTION100
2.3903-2.49910.28461340.20871205X-RAY DIFFRACTION100
2.4991-2.63090.27491340.19581208X-RAY DIFFRACTION100
2.6309-2.79570.2831340.19521206X-RAY DIFFRACTION100
2.7957-3.01150.25931380.19831236X-RAY DIFFRACTION100
3.0115-3.31450.27371360.1841232X-RAY DIFFRACTION100
3.3145-3.79390.21011370.16761229X-RAY DIFFRACTION100
3.7939-4.77920.17211390.1451262X-RAY DIFFRACTION99
4.7792-46.20590.22571520.17361361X-RAY DIFFRACTION99
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.1953-0.1867-0.09090.1530.05370.17380.11870.33340.0624-0.3307-0.131-0.17950.40160.13280.00360.5121-0.0488-0.06920.4321-0.02480.44617.595249.545246.23
20.6806-0.4034-0.14390.42630.31770.94590.06760.0357-0.0588-0.05090.0206-0.1046-0.03970.09470.00020.4536-0.0191-0.00950.39850.01370.467221.332155.369763.4187
30.2203-0.24-0.1630.25560.12860.1361-0.1316-0.25940.02620.2020.1153-0.01430.1932-0.1281-0.00030.54310.0718-0.02890.5138-0.01790.441816.535760.767983.0967
40.2507-0.1906-0.00630.21420.04110.00960.1948-0.2434-0.3270.13810.0148-0.17020.6515-0.2606-0.00070.6771-0.0249-0.0710.46720.06450.561319.841844.059674.8551
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 8 through 45 )
2X-RAY DIFFRACTION2chain 'A' and (resid 46 through 137 )
3X-RAY DIFFRACTION3chain 'A' and (resid 138 through 191 )
4X-RAY DIFFRACTION4chain 'A' and (resid 192 through 227 )

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