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- PDB-6xwu: Crystal structure of drosophila melanogaster CENP-C cumin domain -

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Basic information

Entry
Database: PDB / ID: 6xwu
TitleCrystal structure of drosophila melanogaster CENP-C cumin domain
ComponentsRE68959p
KeywordsCELL CYCLE / Centromere / Kinetochore / Cell division
Function / homology
Function and homology information


regulation of centromere complex assembly / female meiosis chromosome segregation / protein localization to chromosome, centromeric region / kinetochore assembly / condensed chromosome, centromeric region / regulation of stem cell differentiation / protein localization to kinetochore / mitotic metaphase chromosome alignment / chromosome, centromeric region / chromosome segregation / kinetochore
Similarity search - Function
RE68959p / Centromeric protein-C, isoform A
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.82 Å
AuthorsJeyaprakash, A.A. / Medina-Pritchard, B. / Lazou, V. / Zou, J. / Byron, O. / Abad, M.A. / Rappsilber, J. / Heun, P.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Wellcome Trust202811 United Kingdom
CitationJournal: Embo J. / Year: 2020
Title: Structural basis for centromere maintenance by Drosophila CENP-A chaperone CAL1.
Authors: Medina-Pritchard, B. / Lazou, V. / Zou, J. / Byron, O. / Abad, M.A. / Rappsilber, J. / Heun, P. / Jeyaprakash, A.A.
History
DepositionJan 24, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 1, 2020Provider: repository / Type: Initial release
Revision 1.1Apr 8, 2020Group: Database references / Category: citation / Item: _citation.journal_volume
Revision 1.2Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: RE68959p


Theoretical massNumber of molelcules
Total (without water)157,9871
Polymers157,9871
Non-polymers00
Water75742
1
A: RE68959p

A: RE68959p


Theoretical massNumber of molelcules
Total (without water)315,9742
Polymers315,9742
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area3370 Å2
ΔGint-19 kcal/mol
Surface area13290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.195, 57.195, 92.960
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Space group name HallP4abw2nw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+1/4
#3: y+1/2,-x+1/2,z+3/4
#4: x+1/2,-y+1/2,-z+3/4
#5: -x+1/2,y+1/2,-z+1/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2

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Components

#1: Protein RE68959p


Mass: 157987.234 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: CG31258 / Production host: Escherichia coli (E. coli) / References: UniProt: A8WHM0, UniProt: Q9VHP9*PLUS
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 42 / 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

Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: 50mM MES pH6.0, 45% PEG 400

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97625 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 24, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 1.82→28.6 Å / Num. obs: 14427 / % possible obs: 99.73 % / Redundancy: 18 % / Biso Wilson estimate: 32.62 Å2 / Rmerge(I) obs: 0.0548 / Net I/σ(I): 34.13
Reflection shellResolution: 1.82→1.885 Å / Rmerge(I) obs: 0.055 / Num. unique obs: 1392

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
PHENIX1.17.1_3660refinement
XDSdata reduction
Aimlessdata scaling
Cootmodel building
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2VPV

2vpv


Resolution: 1.82→28.6 Å / SU ML: 0.202 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 21.9289
RfactorNum. reflection% reflection
Rfree0.2351 1429 10.01 %
Rwork0.1936 --
obs0.1976 14279 98.61 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 40.88 Å2
Refinement stepCycle: LAST / Resolution: 1.82→28.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1065 0 0 42 1107
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00621082
X-RAY DIFFRACTIONf_angle_d0.85541458
X-RAY DIFFRACTIONf_chiral_restr0.0586163
X-RAY DIFFRACTIONf_plane_restr0.0053189
X-RAY DIFFRACTIONf_dihedral_angle_d5.7741149
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.82-1.880.29481310.23691165X-RAY DIFFRACTION91.53
1.88-1.960.2521360.21251228X-RAY DIFFRACTION97.5
1.96-2.050.23841400.19931257X-RAY DIFFRACTION98.45
2.05-2.160.24751410.20181262X-RAY DIFFRACTION99.22
2.16-2.290.22941430.21111289X-RAY DIFFRACTION99.44
2.29-2.470.23471430.20531281X-RAY DIFFRACTION99.86
2.47-2.720.28321450.21331302X-RAY DIFFRACTION100
2.72-3.110.23721430.21651306X-RAY DIFFRACTION100
3.11-3.920.22011480.18411334X-RAY DIFFRACTION100
3.92-28.60.2251590.17541426X-RAY DIFFRACTION99.87
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)
14.029137159490.4207704375111.378346046837.67759626642-3.625315385817.94517585121-0.3251597108130.3841304926140.9497303738670.303208609821-0.1446863397890.136476309334-0.6031554163770.3990993124740.1852712795250.367290451909-0.0648240799657-0.07257565688990.277397163482-0.04897138075020.45035531664627.839338280134.27259988295.30526399197
23.43148478901-2.63551421232-0.1007850040192.340425679260.06682654358120.150330304701-0.2905389787940.0820319960810.5062411785140.5810710051150.175149086933-0.243043938131-0.3375943344750.007178157133370.1977639729490.421922973255-0.00232184236040.004887908604370.492285876356-0.06996441725460.36363744114517.506743319532.963741213410.511109836
32.70227823117-0.9774089360020.002580894557913.03228939521-1.117628600611.98202213554-0.226786905756-0.514810043954-0.2320236477450.4113318705550.19963560410.1722653961680.0864064645036-0.2566793911830.05092055354720.2853425530730.004375719401110.003719406284970.3704191614990.01837394992860.2420643996221.597443290819.552637113112.4276772057
42.981665783481.208269679931.593366960293.61969322771.27961537562.869525058590.348605452837-0.491659622403-0.0941119421840.596771921019-0.3201861433950.04681359823180.582929069877-0.2232299794090.02748674575480.340022608982-0.0239169654931-0.01131275152840.3431513792870.08885755667630.31175838617228.340669938.126112904519.71786257064
52.819576887131.766784834520.1118720257494.227067193060.4781701899423.14342480739-0.0168793501661-0.1672181389490.071514757745-0.00432287534054-0.0395780141948-0.2142986976370.1586314541790.2132264001060.03021307817620.2229586074560.002059539196150.04487758983260.2669516767650.03305877127510.23039855309630.552070183213.07446634471.76301390965
62.667594785650.1280226893630.0615406164985.660285165190.1651885414331.983870607180.1102865210770.00113374389195-0.450959671286-0.118019223634-0.0592654426348-0.2619688492120.3327887383430.00637571933092-0.02932729669760.325915323430.0193838613280.04879752662130.2314859446430.000674014405870.33406919902330.4869091046.51748222981-2.32364640324
73.034785396990.6383672770940.3621485592974.27372925196-0.2465632071343.317357630490.00920561635217-0.275305567781-0.1632462354690.0332693576273-0.0502046959293-0.1187766965380.187673452491-0.009673993877790.0254049561880.195878255264-0.00490856824779-0.005800680246620.172574187470.01793782983390.21003847336328.651036010111.77488217095.22526064808
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1274 through 1287 )
2X-RAY DIFFRACTION2chain 'A' and (resid 1288 through 1308 )
3X-RAY DIFFRACTION3chain 'A' and (resid 1309 through 1338 )
4X-RAY DIFFRACTION4chain 'A' and (resid 1339 through 1353 )
5X-RAY DIFFRACTION5chain 'A' and (resid 1354 through 1368 )
6X-RAY DIFFRACTION6chain 'A' and (resid 1369 through 1388 )
7X-RAY DIFFRACTION7chain 'A' and (resid 1389 through 1411 )

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