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- PDB-4ld3: Structural analysis of the microcephaly protein CPAP G-box domain... -

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Basic information

Entry
Database: PDB / ID: 4ld3
TitleStructural analysis of the microcephaly protein CPAP G-box domain suggests a role in centriole elongation.
Components
  • SCL-interrupting locus protein homolog
  • Uncharacterized protein
Keywordsstructural protein / protein binding / G-box / beta-sheet / Centriole organisation
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 / body morphogenesis / centriole elongation / regulation of centriole replication / procentriole replication complex / positive regulation of centriole replication / positive regulation of spindle assembly / protein localization to centrosome / smoothened signaling pathway ...TP53 regulates transcription of additional cell cycle genes whose exact role in the p53 pathway remain uncertain / positive regulation of mitotic spindle organization / body morphogenesis / centriole elongation / regulation of centriole replication / procentriole replication complex / positive regulation of centriole replication / positive regulation of spindle assembly / protein localization to centrosome / smoothened signaling pathway / centrosome duplication / cilium assembly / spindle assembly / positive regulation of G1/S transition of mitotic cell cycle / centriole / tubulin binding / mitotic spindle organization / neuron cellular homeostasis / cell cortex / protein domain specific binding / centrosome / cytoplasm / cytosol
Similarity search - Function
lipopolysaccharide transport protein A fold - #20 / SCL-interrupting locus protein / SCL-interrupting locus protein N-terminus / 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
ISOPROPYL ALCOHOL / Centromere protein J / SCL-interrupting locus protein homolog
Similarity search - Component
Biological speciesDanio rerio (zebrafish)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.44 Å
AuthorsHatzopoulos, G.N. / Vakonakis, I.
CitationJournal: Structure / Year: 2013
Title: Structural analysis of the G-box domain of the microcephaly protein CPAP suggests a role in centriole architecture.
Authors: Hatzopoulos, G.N. / Erat, M.C. / Cutts, E. / Rogala, K.B. / Slater, L.M. / Stansfeld, P.J. / Vakonakis, I.
History
DepositionJun 24, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 4, 2013Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2013Group: Database references
Revision 1.2Dec 18, 2013Group: Database references
Revision 1.3Feb 5, 2014Group: Database references
Revision 1.4Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Uncharacterized protein
B: SCL-interrupting locus protein homolog
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,6646
Polymers27,3922
Non-polymers2724
Water543
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)79.396, 79.396, 50.561
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number145
Space group name H-MP32

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Components

#1: Protein Uncharacterized protein


Mass: 20860.330 Da / Num. of mol.: 1 / Fragment: G-box domain (unp residues 942-1121)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Danio rerio (zebrafish) / Gene: cenpj / Production host: Escherichia coli (E. coli) / References: UniProt: E7FCY1
#2: Protein SCL-interrupting locus protein homolog


Mass: 6531.192 Da / Num. of mol.: 1 / Fragment: CPAP interacting fragment (unp residues 398-449)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Danio rerio (zebrafish) / Gene: stil, sill, zgc:110502 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8JGS1
#3: Chemical ChemComp-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL


Mass: 60.095 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O / Comment: alkaloid*YM
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 3 / 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: 3.36 Å3/Da / Density % sol: 63.38 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 15% w/v PEG 4000, 14% v/v isopropanol, 0.1 M Hepes pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: May 19, 2013
RadiationScattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.44→28.87 Å / Num. obs: 13643 / % possible obs: 98 % / Redundancy: 5.1 % / Rmerge(I) obs: 0.066 / Net I/σ(I): 12.7

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Processing

Software
NameVersionClassification
XDSdata scaling
PHASERphasing
BUSTER2.10.0refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.44→28.87 Å / Cor.coef. Fo:Fc: 0.9089 / Cor.coef. Fo:Fc free: 0.8936 / SU R Cruickshank DPI: 0.293 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2144 613 4.98 %RANDOM
Rwork0.1981 ---
obs0.1989 12304 88.53 %-
all-37469 --
Displacement parametersBiso mean: 113.62 Å2
Baniso -1Baniso -2Baniso -3
1-31.0582 Å20 Å20 Å2
2--31.0582 Å20 Å2
3----62.1164 Å2
Refine analyzeLuzzati coordinate error obs: 0.687 Å
Refinement stepCycle: LAST / Resolution: 2.44→28.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1362 0 18 3 1383
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.011410HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.081910HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d639SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes43HARMONIC2
X-RAY DIFFRACTIONt_gen_planes199HARMONIC5
X-RAY DIFFRACTIONt_it1410HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.38
X-RAY DIFFRACTIONt_other_torsion2.74
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion182SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact1474SEMIHARMONIC4
LS refinement shellResolution: 2.44→2.67 Å / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.2338 130 5.33 %
Rwork0.2407 2310 -
all0.2403 2440 -
obs--88.53 %
Refinement TLS params.Method: refined / Origin x: 10.3774 Å / Origin y: 1.9849 Å / Origin z: -7.4509 Å
111213212223313233
T-0.2678 Å20.1926 Å20.0378 Å2--0.461 Å20.0506 Å2--0.1555 Å2
L4.2693 °2-7.5254 °22.4241 °2-13.2609 °2-2.338 °2--2.1996 °2
S0.1636 Å °-0.3353 Å °-0.2775 Å °-0.8618 Å °0.1898 Å °0.3308 Å °0.2188 Å °0.1261 Å °-0.3533 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|953 - A|1106 A|1301 - A|1301 A|1201 - A|1201 A|1203 - A|1203 A|1202 - A|1202 A|1302 - A|1302 A|1204 - A|1204 B|413 - B|428 B|501 - B|501 }A953 - 1106
2X-RAY DIFFRACTION1{ A|953 - A|1106 A|1301 - A|1301 A|1201 - A|1201 A|1203 - A|1203 A|1202 - A|1202 A|1302 - A|1302 A|1204 - A|1204 B|413 - B|428 B|501 - B|501 }A1301
3X-RAY DIFFRACTION1{ A|953 - A|1106 A|1301 - A|1301 A|1201 - A|1201 A|1203 - A|1203 A|1202 - A|1202 A|1302 - A|1302 A|1204 - A|1204 B|413 - B|428 B|501 - B|501 }A1201
4X-RAY DIFFRACTION1{ A|953 - A|1106 A|1301 - A|1301 A|1201 - A|1201 A|1203 - A|1203 A|1202 - A|1202 A|1302 - A|1302 A|1204 - A|1204 B|413 - B|428 B|501 - B|501 }A1203
5X-RAY DIFFRACTION1{ A|953 - A|1106 A|1301 - A|1301 A|1201 - A|1201 A|1203 - A|1203 A|1202 - A|1202 A|1302 - A|1302 A|1204 - A|1204 B|413 - B|428 B|501 - B|501 }A1202
6X-RAY DIFFRACTION1{ A|953 - A|1106 A|1301 - A|1301 A|1201 - A|1201 A|1203 - A|1203 A|1202 - A|1202 A|1302 - A|1302 A|1204 - A|1204 B|413 - B|428 B|501 - B|501 }A1302
7X-RAY DIFFRACTION1{ A|953 - A|1106 A|1301 - A|1301 A|1201 - A|1201 A|1203 - A|1203 A|1202 - A|1202 A|1302 - A|1302 A|1204 - A|1204 B|413 - B|428 B|501 - B|501 }A1204
8X-RAY DIFFRACTION1{ A|953 - A|1106 A|1301 - A|1301 A|1201 - A|1201 A|1203 - A|1203 A|1202 - A|1202 A|1302 - A|1302 A|1204 - A|1204 B|413 - B|428 B|501 - B|501 }B413 - 428
9X-RAY DIFFRACTION1{ A|953 - A|1106 A|1301 - A|1301 A|1201 - A|1201 A|1203 - A|1203 A|1202 - A|1202 A|1302 - A|1302 A|1204 - A|1204 B|413 - B|428 B|501 - B|501 }B501

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