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- PDB-4bxq: Structure of the E1021V mutant of the TCP10 domain of Danio rerio CPAP -

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Basic information

Entry
Database: PDB / ID: 4bxq
TitleStructure of the E1021V mutant of the 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
Centrosomal P4.1-associated protein
Similarity search - Component
Biological speciesDANIO RERIO (zebrafish)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.9 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 1.3Apr 4, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type
Revision 1.4Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
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)21,8621
Polymers21,8621
Non-polymers00
Water2,054114
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)52.120, 36.480, 56.460
Angle α, β, γ (deg.)90.00, 117.47, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein CPAP


Mass: 21861.557 Da / Num. of mol.: 1 / Fragment: TCP-10 DOMAIN, RESIDUE 937-1124 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) DANIO RERIO (zebrafish) / 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.: 114 / 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: 2.18 Å3/Da / Density % sol: 43.6 % / Description: NONE
Crystal growpH: 8.5
Details: 80 MM TRIS PH 8.5, 160 MM MGCL2, 24% PEG-4000, 20% GLYCEROL

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E / Wavelength: 1.5418
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Nov 11, 2010 / Details: MULTILAYER FOCUSSING OPTICS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.9→36.5 Å / Num. obs: 15136 / % possible obs: 100 % / Observed criterion σ(I): 1.8 / Redundancy: 6.8 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 13.8
Reflection shellResolution: 1.9→2 Å / Redundancy: 6.6 % / Rmerge(I) obs: 1.09 / Mean I/σ(I) obs: 1.8 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.7.0032refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4BXP

4bxp


Resolution: 1.9→29.49 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.926 / SU B: 4.329 / SU ML: 0.124 / Cross valid method: THROUGHOUT / ESU R: 0.173 / ESU R Free: 0.168 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.26682 762 5 %RANDOM
Rwork0.20913 ---
obs0.21212 14349 99.88 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 31.553 Å2
Baniso -1Baniso -2Baniso -3
1-1.29 Å20 Å2-0.06 Å2
2--0.89 Å20 Å2
3----1.39 Å2
Refinement stepCycle: LAST / Resolution: 1.9→29.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1372 0 0 114 1486
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0191436
X-RAY DIFFRACTIONr_bond_other_d0.0010.021360
X-RAY DIFFRACTIONr_angle_refined_deg1.311.9531950
X-RAY DIFFRACTIONr_angle_other_deg0.71833142
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2675180
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.35724.13375
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.07115255
X-RAY DIFFRACTIONr_dihedral_angle_4_deg24.4111512
X-RAY DIFFRACTIONr_chiral_restr0.0730.2211
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0211648
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02338
X-RAY DIFFRACTIONr_nbd_refined0.2510.2305
X-RAY DIFFRACTIONr_nbd_other0.1820.21201
X-RAY DIFFRACTIONr_nbtor_refined0.1710.2652
X-RAY DIFFRACTIONr_nbtor_other0.0770.2859
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.170.255
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.060.21
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2060.224
X-RAY DIFFRACTIONr_symmetry_vdw_other0.160.265
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1890.27
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.0352.96693
X-RAY DIFFRACTIONr_mcbond_other2.0362.958692
X-RAY DIFFRACTIONr_mcangle_it3.364.424867
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.2953.257743
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.7474.7761078
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: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.409 54 -
Rwork0.345 1056 -
obs--100 %

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