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- PDB-4bxp: Structure of the wild-type TCP10 domain of Danio rerio CPAP -

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Basic information

Entry
Database: PDB / ID: 4bxp
TitleStructure of the wild-type TCP10 domain of Danio rerio CPAP
ComponentsCPAP
KeywordsCELL CYCLE / CENTRIOLE DUPLICATION
Function / homology
Function and homology information


TP53 regulates transcription of additional cell cycle genes whose exact role in the p53 pathway remain uncertain / positive regulation of mitotic spindle organization / centriole elongation / procentriole replication complex / positive regulation of centriole replication / positive regulation of spindle assembly / cilium assembly / positive regulation of G1/S transition of mitotic cell cycle / centriole / tubulin binding ...TP53 regulates transcription of additional cell cycle genes whose exact role in the p53 pathway remain uncertain / positive regulation of mitotic spindle organization / centriole elongation / procentriole replication complex / positive regulation of centriole replication / positive regulation of spindle assembly / cilium assembly / positive regulation of G1/S transition of mitotic cell cycle / centriole / tubulin binding / protein domain specific binding / centrosome / cytoplasm
Similarity search - Function
lipopolysaccharide transport protein A fold - #20 / T-complex protein 10, C-terminal domain / T-complex protein 10 family / T-complex protein 10 C-terminus / lipopolysaccharide transport protein A fold / : / Sandwich / Mainly Beta
Similarity search - Domain/homology
Centromere protein J
Similarity search - Component
Biological speciesDANIO RERIO (zebrafish)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.7 Å
Authorsvan Breugel, M.
CitationJournal: Elife / Year: 2013
Title: Crystal structures of the CPAP/STIL complex reveal its role in centriole assembly and human microcephaly.
Authors: Cottee, M.A. / Muschalik, N. / Wong, Y.L. / Johnson, C.M. / Johnson, S. / Andreeva, A. / Oegema, K. / Lea, S.M. / Raff, J.W. / van Breugel, M.
History
DepositionJul 15, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 25, 2013Provider: repository / Type: Initial release
Revision 1.1Oct 2, 2013Group: Database references
Revision 1.2Jan 17, 2018Group: Database references / Category: citation / citation_author
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _citation_author.name
Revision 1.3May 8, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CPAP


Theoretical massNumber of molelcules
Total (without water)21,8921
Polymers21,8921
Non-polymers00
Water3,423190
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)52.340, 36.440, 56.440
Angle α, β, γ (deg.)90.00, 117.31, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein CPAP


Mass: 21891.539 Da / Num. of mol.: 1 / Fragment: TCP-10 DOMAIN, RESIDUES 937-1124
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) DANIO RERIO (zebrafish) / Description: CDNA / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): ROSETTA / References: UniProt: E7FCY1
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 190 / 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

CrystalDensity Matthews: 2.19 Å3/Da / Density % sol: 43.8 % / Description: NONE
Crystal growpH: 8.5
Details: 80 MM TRIS PH 8.5, 160 MM MGCL2, 20% PEG4K, 18 % GLYCEROL, 1MM DTT

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9786
DetectorType: ADSC CCD / Detector: CCD / Date: Oct 9, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9786 Å / Relative weight: 1
ReflectionResolution: 1.7→29.5 Å / Num. obs: 21047 / % possible obs: 99.7 % / Observed criterion σ(I): 2 / Redundancy: 7.2 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 14.6
Reflection shellResolution: 1.7→1.79 Å / Redundancy: 7.3 % / Rmerge(I) obs: 0.93 / Mean I/σ(I) obs: 2 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.7.0029refinement
MOSFLMdata reduction
SCALAdata scaling
CRANKphasing
RefinementMethod to determine structure: MAD
Starting model: NONE

Resolution: 1.7→28.68 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.942 / SU B: 2.614 / SU ML: 0.086 / Cross valid method: THROUGHOUT / ESU R: 0.118 / ESU R Free: 0.119 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.24373 1075 5.1 %RANDOM
Rwork0.19919 ---
obs0.20151 19941 99.56 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 26.516 Å2
Baniso -1Baniso -2Baniso -3
1-1.18 Å20 Å2-0.14 Å2
2--1.09 Å20 Å2
3----1.43 Å2
Refinement stepCycle: LAST / Resolution: 1.7→28.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1371 0 0 190 1561
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0191441
X-RAY DIFFRACTIONr_bond_other_d0.0010.021361
X-RAY DIFFRACTIONr_angle_refined_deg1.4781.9531959
X-RAY DIFFRACTIONr_angle_other_deg0.7733145
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6275181
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.74624.28677
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.44515257
X-RAY DIFFRACTIONr_dihedral_angle_4_deg26.9811512
X-RAY DIFFRACTIONr_chiral_restr0.0820.2211
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0211664
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02342
X-RAY DIFFRACTIONr_nbd_refined0.270.2398
X-RAY DIFFRACTIONr_nbd_other0.1810.21220
X-RAY DIFFRACTIONr_nbtor_refined0.170.2659
X-RAY DIFFRACTIONr_nbtor_other0.0810.2879
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1080.259
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3320.244
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1810.263
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1340.27
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.0732.5511441
X-RAY DIFFRACTIONr_mcbond_other0.482.621361
X-RAY DIFFRACTIONr_mcangle_it3.3413.7791953
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.294 75 -
Rwork0.272 1467 -
obs--99.94 %

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