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- PDB-6fvi: ASH / PapD-like domain of human CEP192 (PapD-like domain 7) -

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Basic information

Entry
Database: PDB / ID: 6fvi
TitleASH / PapD-like domain of human CEP192 (PapD-like domain 7)
ComponentsCentrosomal protein of 192 kDa
KeywordsCELL CYCLE / Centrosome / centriole / PapD-like domain / ASH domain
Function / homology
Function and homology information


centrosome-templated microtubule nucleation / procentriole / procentriole replication complex / centrosome cycle / protein localization to centrosome / pericentriolar material / centriole replication / mitotic spindle assembly / phosphatase binding / centriole ...centrosome-templated microtubule nucleation / procentriole / procentriole replication complex / centrosome cycle / protein localization to centrosome / pericentriolar material / centriole replication / mitotic spindle assembly / phosphatase binding / centriole / Loss of Nlp from mitotic centrosomes / Loss of proteins required for interphase microtubule organization from the centrosome / Recruitment of mitotic centrosome proteins and complexes / Recruitment of NuMA to mitotic centrosomes / Anchoring of the basal body to the plasma membrane / AURKA Activation by TPX2 / response to bacterium / Regulation of PLK1 Activity at G2/M Transition / centrosome / cytosol / cytoplasm
Similarity search - Function
Centrosomal protein Spd-2/CEP192 / : / : / : / : / : / Cep192 domain 1 / Cep192 domain 2 / Cep192 domain 7 / Cep192 domain 8 ...Centrosomal protein Spd-2/CEP192 / : / : / : / : / : / Cep192 domain 1 / Cep192 domain 2 / Cep192 domain 7 / Cep192 domain 8 / Cep192 domain 3 / : / : / : / Cep192 domain 4 / Cep192 domain 5 / Cep192 domain 6 / Immunoglobulin-like fold
Similarity search - Domain/homology
Centrosomal protein of 192 kDa
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1 Å
AuthorsKovalevskiy, O.V. / van Breugel, M.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Medical Research Council (United Kingdom)MC_UP_1201/3 United Kingdom
CitationJournal: To Be Published
Title: ASH / PapD-like domain of human CEP192 (PapD-like domain 7)
Authors: Kovalevskiy, O. / van Breugel, M.
History
DepositionMar 2, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 20, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 13, 2024Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / refine_hist
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine_hist.d_res_low

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Centrosomal protein of 192 kDa
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,9862
Polymers16,9511
Non-polymers351
Water3,567198
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area140 Å2
ΔGint-9 kcal/mol
Surface area9340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.700, 60.060, 64.110
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP22121
Components on special symmetry positions
IDModelComponents
11A-2040-

HOH

21A-2100-

HOH

31A-2139-

HOH

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Components

#1: Protein Centrosomal protein of 192 kDa / Cep192


Mass: 16950.646 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CEP192, KIAA1569, PP8407 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8TEP8
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 198 / 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: 2.25 Å3/Da / Density % sol: 45.44 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 100 mM Na-Citrate, pH 5.5, 30 % (v/v) PEG-400, 100 mM NaCl, 100 mM MgCl2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.72932 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Apr 12, 2015
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.72932 Å / Relative weight: 1
ReflectionResolution: 1→23.03 Å / Num. obs: 82358 / % possible obs: 98.8 % / Redundancy: 14.8 % / CC1/2: 0.999 / Rmerge(I) obs: 0.071 / Rpim(I) all: 0.019 / Rrim(I) all: 0.074 / Net I/σ(I): 18.2 / Num. measured all: 1218883 / Scaling rejects: 90
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1-1.0214.81.3766080641080.6780.3681.4252.397.2
5.39-23.03120.04169295790.9990.0120.04345.292

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Processing

Software
NameVersionClassification
REFMACrefinement
Aimless0.5.28data scaling
PDB_EXTRACT3.24data extraction
MOSFLMdata reduction
CRANKphasing
RefinementMethod to determine structure: MAD / Resolution: 1→23.03 Å / Cor.coef. Fo:Fc: 0.977 / Cor.coef. Fo:Fc free: 0.975 / WRfactor Rfree: 0.1507 / WRfactor Rwork: 0.1329 / FOM work R set: 0.9045 / SU B: 0.655 / SU ML: 0.015 / SU R Cruickshank DPI: 0.0227 / SU Rfree: 0.0227 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.023 / ESU R Free: 0.023 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1518 3965 4.8 %RANDOM
Rwork0.1364 ---
obs0.1372 78331 98.57 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 388.59 Å2 / Biso mean: 15.199 Å2 / Biso min: 0.53 Å2
Baniso -1Baniso -2Baniso -3
1-0.33 Å20 Å2-0 Å2
2---0.53 Å20 Å2
3---0.2 Å2
Refinement stepCycle: final / Resolution: 1→23.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1111 0 1 215 1327
Biso mean--12.91 38.53 -
Num. residues----142
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0191532
X-RAY DIFFRACTIONr_bond_other_d0.0020.021406
X-RAY DIFFRACTIONr_angle_refined_deg1.8271.9762122
X-RAY DIFFRACTIONr_angle_other_deg1.07333328
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9675220
X-RAY DIFFRACTIONr_dihedral_angle_2_deg27.2223.73167
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.34615268
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.5751511
X-RAY DIFFRACTIONr_chiral_restr0.110.2234
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0211788
X-RAY DIFFRACTIONr_gen_planes_other0.0040.02311
X-RAY DIFFRACTIONr_rigid_bond_restr1.90532937
X-RAY DIFFRACTIONr_sphericity_free30.818592
X-RAY DIFFRACTIONr_sphericity_bonded26.94652994
LS refinement shellResolution: 1→1.026 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.269 292 -
Rwork0.251 5615 -
all-5907 -
obs--97.39 %

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