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- PDB-4wau: Crystal structure of CENP-M solved by native-SAD phasing -

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Basic information

Entry
Database: PDB / ID: 4wau
TitleCrystal structure of CENP-M solved by native-SAD phasing
ComponentsCentromere protein M
KeywordsCELL CYCLE / native-SAD / S-SAD / sulfur-SAD / sulfur SAD / Mitosis / Kinetochore / CCAN / G-protein
Function / homology
Function and homology information


inner kinetochore / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / Deposition of new CENPA-containing nucleosomes at the centromere / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / Resolution of Sister Chromatid Cohesion / chromosome segregation / RHO GTPases Activate Formins / Separation of Sister Chromatids / nucleoplasm ...inner kinetochore / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / Deposition of new CENPA-containing nucleosomes at the centromere / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / Resolution of Sister Chromatid Cohesion / chromosome segregation / RHO GTPases Activate Formins / Separation of Sister Chromatids / nucleoplasm / nucleus / cytosol
Similarity search - Function
Centromere protein Cenp-M / Centromere protein M (CENP-M) / P-loop containing nucleotide triphosphate hydrolases / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Centromere protein M
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.2 Å
AuthorsWeinert, T. / Basilico, F. / Cecatiello, V. / Pasqualato, S. / Wang, M.
CitationJournal: Nat.Methods / Year: 2015
Title: Fast native-SAD phasing for routine macromolecular structure determination.
Authors: Weinert, T. / Olieric, V. / Waltersperger, S. / Panepucci, E. / Chen, L. / Zhang, H. / Zhou, D. / Rose, J. / Ebihara, A. / Kuramitsu, S. / Li, D. / Howe, N. / Schnapp, G. / Pautsch, A. / ...Authors: Weinert, T. / Olieric, V. / Waltersperger, S. / Panepucci, E. / Chen, L. / Zhang, H. / Zhou, D. / Rose, J. / Ebihara, A. / Kuramitsu, S. / Li, D. / Howe, N. / Schnapp, G. / Pautsch, A. / Bargsten, K. / Prota, A.E. / Surana, P. / Kottur, J. / Nair, D.T. / Basilico, F. / Cecatiello, V. / Pasqualato, S. / Boland, A. / Weichenrieder, O. / Wang, B.C. / Steinmetz, M.O. / Caffrey, M. / Wang, M.
History
DepositionSep 1, 2014Deposition site: RCSB / Processing site: PDBE
Revision 1.0Dec 10, 2014Provider: repository / Type: Initial release
Revision 1.1Dec 31, 2014Group: Database references
Revision 1.2Feb 11, 2015Group: Database references
Revision 1.3May 8, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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: Centromere protein M
B: Centromere protein M


Theoretical massNumber of molelcules
Total (without water)38,4912
Polymers38,4912
Non-polymers00
Water6,143341
1
A: Centromere protein M


Theoretical massNumber of molelcules
Total (without water)19,2451
Polymers19,2451
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Centromere protein M


Theoretical massNumber of molelcules
Total (without water)19,2451
Polymers19,2451
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)104.570, 104.570, 33.580
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number143
Space group name H-MP3

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Components

#1: Protein Centromere protein M / CENP-M / Interphase centromere complex protein 39 / Proliferation-associated nuclear element protein 1


Mass: 19245.443 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: residue 62 can not be observed in the density, however the density for the whole loop region is not very good.
Source: (gene. exp.) Homo sapiens (human) / Gene: CENPM, C22orf18, ICEN39, PANE1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9NSP4
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 341 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.75 Å3/Da / Density % sol: 55.34 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / Details: 100 mM bicine pH 8.5, 11 % MPD, 8 mM spermidine / PH range: 8.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 2.0664 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Dec 10, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 2.0664 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. obs: 40969 / % possible obs: 98.1 % / Redundancy: 140.4 % / Net I/σ(I): 92.37
Reflection shellResolution: 2.2→2.26 Å / Redundancy: 32.3 % / Rmerge(I) obs: 0.139 / Mean I/σ(I) obs: 16.94 / % possible all: 86.8

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.9_1692)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: SAD / Resolution: 2.2→45.28 Å / Cross valid method: FREE R-VALUE / σ(F): 1.7 / Phase error: 14.5 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflection
Rfree0.1476 2117 5.17 %
Rwork0.1168 --
obs0.1252 40969 98.14 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.2→45.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2351 0 0 341 2692
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0022390
X-RAY DIFFRACTIONf_angle_d0.5513241
X-RAY DIFFRACTIONf_dihedral_angle_d11.567869
X-RAY DIFFRACTIONf_chiral_restr0.02400
X-RAY DIFFRACTIONf_plane_restr0.002406
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2001-2.25130.17931240.11552292X-RAY DIFFRACTION82
2.2513-2.30750.1641480.11992500X-RAY DIFFRACTION91
2.3075-2.36990.17011390.12942496X-RAY DIFFRACTION90
2.3699-2.43950.16431720.12712612X-RAY DIFFRACTION91
2.4395-2.51820.16211520.14222526X-RAY DIFFRACTION94
2.5182-2.60810.17471430.14722647X-RAY DIFFRACTION93
2.6081-2.71240.1751260.13972590X-RAY DIFFRACTION95
2.7124-2.83560.18091460.13242653X-RAY DIFFRACTION95
2.8356-2.98490.14321300.12642638X-RAY DIFFRACTION95
2.9849-3.17150.16171500.12692646X-RAY DIFFRACTION95
3.1715-3.41570.12841580.12472614X-RAY DIFFRACTION94
3.4157-3.75830.14531100.11512700X-RAY DIFFRACTION96
3.7583-4.29940.14481340.10232612X-RAY DIFFRACTION95
4.2994-5.40650.12691300.10352652X-RAY DIFFRACTION95
5.4065-23.97210.16341500.14162636X-RAY DIFFRACTION95

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