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- PDB-6o2k: Drosophila melanogaster CENP-C cupin domain -

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Basic information

Entry
Database: PDB / ID: 6o2k
TitleDrosophila melanogaster CENP-C cupin domain
ComponentsCentromeric protein-C, isoform A
KeywordsCELL CYCLE / Cupin / Kinetochore / CENP-C / Drosophila / dimer
Function / homology
Function and homology information


regulation of stem cell differentiation / regulation of centromere complex assembly / kinetochore assembly / condensed chromosome, centromeric region / protein localization to chromosome, centromeric region / female meiosis chromosome segregation / protein localization to kinetochore / mitotic metaphase plate congression / chromosome, centromeric region / kinetochore / chromosome segregation
Similarity search - Function
Centromeric protein-C, isoform A
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.81 Å
AuthorsChik, J.K. / Cho, U.S.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)R01-DK111465 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)T32-GM007315 United States
CitationJournal: J.Biol.Chem. / Year: 2019
Title: Structures of CENP-C cupin domains at regional centromeres reveal unique patterns of dimerization and recruitment functions for the inner pocket.
Authors: Chik, J.K. / Moiseeva, V. / Goel, P.K. / Meinen, B.A. / Koldewey, P. / An, S. / Mellone, B.G. / Subramanian, L. / Cho, U.S.
History
DepositionFeb 23, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 21, 2019Provider: repository / Type: Initial release
Revision 1.1Sep 25, 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.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Oct 2, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Centromeric protein-C, isoform A
B: Centromeric protein-C, isoform A


Theoretical massNumber of molelcules
Total (without water)32,1472
Polymers32,1472
Non-polymers00
Water2,306128
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: equilibrium centrifugation
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3610 Å2
ΔGint-17 kcal/mol
Surface area13500 Å2
MethodPISA
Unit cell
γ
α
β
Length a, b, c (Å)51.930, 61.720, 87.920
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Centromeric protein-C, isoform A


Mass: 16073.384 Da / Num. of mol.: 2 / Fragment: Cupin Domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly)
Gene: Cenp-C, CENP-C, cenp-C, Cenp-C-RA, CenpC, CG11745, CG11746, CLD1, Dmel\CG31258, l(2)SH3 157, l(3)85Aa, l(3)SH157, L1, CG31258, Dmel_CG31258
Production host: Escherichia coli (E. coli) / References: UniProt: Q9VHP9
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 128 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsThe construct used for crystallization was D. melanogaster CENP-C 1190-1411 with an additional Ser- ...The construct used for crystallization was D. melanogaster CENP-C 1190-1411 with an additional Ser-Asn-Ala sequence at the N-terminus from the expression tag. Tag and residues 1190-1269 were likely proteolytically cleaved during crystallization and are not visible in the structure.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

Crystal
IDDensity Matthews3/Da)Density % sol (%)
12.1943.87
2
Crystal grow
Temperature (K)Crystal-IDMethodDetails
298.151vapor diffusion, hanging dropPurified native D. Melanogaster CENPC 1244 to 1411 protein was mixed with 0.2 M NaCl, 0.1 M MES (pH 6.0), 15 % v/v Pentaerythritol propoxylate (5/4 PO/OH) in a 1:1 ratio (v/v). SeMet substituted crystals were grown in the same condition by providing native crystals as microseeds
298.152vapor diffusion, hanging dropD. melanogaster CENP-C 1190-1411 crystals were grown by mixing purified proteins 0.1 M MOPS (pH 7.0) and 12% (w/v) PEG 4000 in a 1:1 ratio (v/v)

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Data collection

Diffraction
IDMean temperature (K)Crystal-IDSerial crystal experiment
11051N
21052N
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONAPS 21-ID-G10.9786
SYNCHROTRONAPS 21-ID-G20.9786
Detector
TypeIDDetectorDate
MARMOSAIC 300 mm CCD1CCDAug 16, 2018
MARMOSAIC 300 mm CCD2CCDAug 15, 2017
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2SINGLE WAVELENGTHMx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
10.97861
21
Reflection

Entry-ID: 6O2K

Resolution (Å)Num. obs% possible obs (%)Redundancy (%)Rpim(I) allDiffraction-IDNet I/σ(I)
1.81-30.862638599.64.80.02221.6
2.63-40.251482399.921.80.056111.8
Reflection shell
Resolution (Å)Num. unique obsRpim(I) allDiffraction-ID
1.81-1.8619240.2572
2.63-2.710760.5021

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Processing

Software
NameVersionClassification
Aimlessdata scaling
MOSFLMdata reduction
XDSdata reduction
AutoSolphasing
Cootmodel building
PHENIX(1.14_3260: ???)refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.81→30.86 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 24.7
RfactorNum. reflection% reflection
Rfree0.2317 1914 7.61 %
Rwork0.1955 --
obs0.1983 25138 95.08 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.81→30.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2186 0 0 128 2314
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072266
X-RAY DIFFRACTIONf_angle_d0.9023059
X-RAY DIFFRACTIONf_dihedral_angle_d10.3591960
X-RAY DIFFRACTIONf_chiral_restr0.07337
X-RAY DIFFRACTIONf_plane_restr0.005400
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.81-1.85530.3161320.27621478X-RAY DIFFRACTION86
1.8553-1.90540.351200.23711501X-RAY DIFFRACTION89
1.9054-1.96150.24281250.21751553X-RAY DIFFRACTION90
1.9615-2.02480.26871290.21731587X-RAY DIFFRACTION92
2.0248-2.09710.27451310.20381601X-RAY DIFFRACTION94
2.0971-2.18110.24161320.19941647X-RAY DIFFRACTION95
2.1811-2.28030.27871380.19721652X-RAY DIFFRACTION96
2.2803-2.40050.24361380.20231670X-RAY DIFFRACTION97
2.4005-2.55080.26431420.21781699X-RAY DIFFRACTION98
2.5508-2.74770.2471400.2221711X-RAY DIFFRACTION98
2.7477-3.0240.26541440.22461730X-RAY DIFFRACTION99
3.024-3.4610.21251440.20551750X-RAY DIFFRACTION99
3.461-4.35860.19061460.16471777X-RAY DIFFRACTION100
4.3586-30.86450.19481530.16061868X-RAY DIFFRACTION99
Refinement TLS params.

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

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
11.87621.4316-0.12682.0898-0.43641.1438-0.06520.0174-0.1755-0.2094-0.0457-0.12550.08880.11580.09550.17560.04090.01020.1801-0.0090.1347-13.98669.1922-16.595
21.85260.89580.10861.338-0.04030.83910.116-0.429-0.18070.1679-0.1481-0.0856-0.02750.04850.0240.18070.0112-0.01590.23960.02140.1507-20.90421.9441-2.139
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain 'A' and resid 1273 through 1411)
2X-RAY DIFFRACTION2(chain 'B' and resid 1270 through 1411)

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