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- PDB-7bji: Crystal structure of the Danio rerio centrosomal protein Cep135 c... -

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Basic information

Entry
Database: PDB / ID: 7bji
TitleCrystal structure of the Danio rerio centrosomal protein Cep135 coiled-coil fragment 64-190
ComponentsCentrosomal protein of 135 kDa
KeywordsSTRUCTURAL PROTEIN / centriole / centrosome / coiled coil / pinehead / alpha helix
Function / homology: / centriole replication / centriole / centrosome / cytoplasm / ACETATE ION / TRIETHYLENE GLYCOL / Centrosomal protein of 135 kDa
Function and homology information
Biological speciesDanio rerio (zebrafish)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.58 Å
AuthorsLi, Q. / Hatzopoulos, G. / Iller, O. / Vakonakis, I.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Medical Research Council (MRC, United Kingdom)MR/N009274/1 United Kingdom
CitationJournal: To Be Published
Title: Crystal structure of the Danio rerio centrosomal protein Cep135 coiled-coil fragment 64-190
Authors: Li, Q. / Hatzopoulos, G. / Iller, O. / Vakonakis, I.
History
DepositionJan 14, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 27, 2021Provider: repository / Type: Initial release
Revision 1.1May 15, 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

Downloads & links

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Assembly

Deposited unit
A: Centrosomal protein of 135 kDa
B: Centrosomal protein of 135 kDa
C: Centrosomal protein of 135 kDa
D: Centrosomal protein of 135 kDa
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,66914
Polymers59,9374
Non-polymers73310
Water1448
1
A: Centrosomal protein of 135 kDa
C: Centrosomal protein of 135 kDa
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,5159
Polymers29,9682
Non-polymers5477
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5420 Å2
ΔGint-34 kcal/mol
Surface area12520 Å2
MethodPISA
2
B: Centrosomal protein of 135 kDa
D: Centrosomal protein of 135 kDa
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,1555
Polymers29,9682
Non-polymers1863
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5260 Å2
ΔGint-40 kcal/mol
Surface area14200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)103.290, 188.220, 89.970
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number21
Space group name H-MC222

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
Centrosomal protein of 135 kDa / Cep135


Mass: 14984.168 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Danio rerio (zebrafish) / Gene: cep135, si:dkeyp-117h8.1 / Plasmid: pFLOAT / Details (production host): pET30a derivative / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q5RG45

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Non-polymers , 5 types, 18 molecules

#2: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 18.015 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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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: 3.65 Å3/Da / Density % sol: 66.28 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 4
Details: 15 mg/ml DrCep135 64-190 in 20 mM HEPES pH 7.5, 150 mM NaCl, 0.5 mM TCEP; 0.2 M ammonium acetate, 0.1 M sodium acetate, 15% w/v PEG 4000, pH 4 mother liquor; 1:2 protein / mother liquor ratio, 300nl drops

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 3, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 2.58→89.97 Å / Num. obs: 28078 / % possible obs: 99.9 % / Redundancy: 6.6 % / Biso Wilson estimate: 87.85 Å2 / CC1/2: 1 / Rrim(I) all: 0.091 / Net I/σ(I): 12.5
Reflection shellResolution: 2.58→2.62 Å / Redundancy: 6.9 % / Mean I/σ(I) obs: 1.1 / Num. unique obs: 1392 / CC1/2: 0.5 / Rrim(I) all: 1.9 / % possible all: 100

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Processing

Software
NameVersionClassification
BUSTER2.10.3refinement
XDSdata reduction
pointlessdata scaling
SHELXDEphasing
RefinementMethod to determine structure: SAD / Resolution: 2.58→63.82 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.908 / SU R Cruickshank DPI: 0.257 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.249 / SU Rfree Blow DPI: 0.203 / SU Rfree Cruickshank DPI: 0.209
RfactorNum. reflection% reflectionSelection details
Rfree0.249 1287 4.58 %RANDOM
Rwork0.233 ---
obs0.234 28075 99.9 %-
Displacement parametersBiso mean: 124.39 Å2
Baniso -1Baniso -2Baniso -3
1--2.4374 Å20 Å20 Å2
2---5.2091 Å20 Å2
3---7.6465 Å2
Refine analyzeLuzzati coordinate error obs: 0.42 Å
Refinement stepCycle: 1 / Resolution: 2.58→63.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2881 0 48 8 2937
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.012981HARMONIC2
X-RAY DIFFRACTIONt_angle_deg13965HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1209SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes516HARMONIC5
X-RAY DIFFRACTIONt_it2981HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.24
X-RAY DIFFRACTIONt_other_torsion18.68
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion369SEMIHARMONIC5
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_contact3222SEMIHARMONIC4
LS refinement shellResolution: 2.58→2.6 Å / Total num. of bins used: 50
RfactorNum. reflection% reflection
Rfree0.2211 -3.91 %
Rwork0.2341 540 -
all0.2336 562 -
obs--99.82 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.4093.4725-1.521313.4373-1.88721.05980.0374-0.1017-0.9621.1484-0.166-0.00880.1326-0.03250.1286-0.9458-0.0188-0.0517-1.02870.097-0.671623.777318.913289.4092
20.0928-0.0521-0.7380.7038-2.835211.97110.0627-0.6407-0.02940.1621-0.2295-0.13460.87920.23960.1668-0.7442-0.293-0.11-0.25690.169-0.981144.895230.1483124.898
33.69792.3297-2.566911.4195-4.79884.1075-0.08760.1163-0.86020.2850.19451.53330.4895-0.1182-0.1069-0.91280.06130.0689-0.95720.0294-0.330920.15625.162485.7184
40.2222-0.50541.00941.3914-5.953428.96260.09-0.5041-0.26730.35130.42410.08730.0255-2.5465-0.5141-0.9083-0.2524-0.078-0.44750.2524-1.026641.724330.3648126.466
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|* }
2X-RAY DIFFRACTION2{ B|* }
3X-RAY DIFFRACTION3{ C|* }
4X-RAY DIFFRACTION4{ D|* }

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