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- PDB-4jon: Crystal structure of a centrosomal protein 170kDa, transcript var... -

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Basic information

Entry
Database: PDB / ID: 4jon
TitleCrystal structure of a centrosomal protein 170kDa, transcript variant beta (CEP170) from Homo sapiens at 2.15 A resolution (PSI Community Target, Sundstrom)
ComponentsCentrosomal protein of 170 kDaCentrosome
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / FHA domain / PF00498 / putative protein-protein recognition / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-BIOLOGY
Function / homology
Function and homology information


centriolar subdistal appendage / centriole / mitotic spindle / microtubule / centrosome / cytosol
Similarity search - Function
Centrosomal protein of 170kDa / CEP170, C-terminal / CEP170 C-terminus / Tumour Suppressor Smad4 - #20 / Tumour Suppressor Smad4 / Forkhead associated domain / Forkhead-associated (FHA) domain profile. / FHA domain / Forkhead-associated (FHA) domain / SMAD/FHA domain superfamily ...Centrosomal protein of 170kDa / CEP170, C-terminal / CEP170 C-terminus / Tumour Suppressor Smad4 - #20 / Tumour Suppressor Smad4 / Forkhead associated domain / Forkhead-associated (FHA) domain profile. / FHA domain / Forkhead-associated (FHA) domain / SMAD/FHA domain superfamily / Sandwich / Mainly Beta
Similarity search - Domain/homology
Centrosomal protein of 170 kDa
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.15 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of a centrosomal protein 170kDa, transcript variant beta (CEP170) from Homo sapiens at 2.15 A resolution (PSI Community Target, Sundstrom)
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionMar 18, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 17, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.2Jan 24, 2018Group: Database references / Category: citation_author / Item: _citation_author.name
Revision 1.3Feb 1, 2023Group: Database references / Derived calculations / Category: 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

Downloads & links

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Assembly

Deposited unit
A: Centrosomal protein of 170 kDa
B: Centrosomal protein of 170 kDa
C: Centrosomal protein of 170 kDa
D: Centrosomal protein of 170 kDa
E: Centrosomal protein of 170 kDa
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,0106
Polymers72,9185
Non-polymers921
Water5,332296
1
A: Centrosomal protein of 170 kDa


Theoretical massNumber of molelcules
Total (without water)14,5841
Polymers14,5841
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Centrosomal protein of 170 kDa
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,6762
Polymers14,5841
Non-polymers921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Centrosomal protein of 170 kDa


Theoretical massNumber of molelcules
Total (without water)14,5841
Polymers14,5841
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Centrosomal protein of 170 kDa


Theoretical massNumber of molelcules
Total (without water)14,5841
Polymers14,5841
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: Centrosomal protein of 170 kDa


Theoretical massNumber of molelcules
Total (without water)14,5841
Polymers14,5841
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)95.040, 183.332, 97.268
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein
Centrosomal protein of 170 kDa / Centrosome / Cep170 / KARP-1-binding protein / KARP1-binding protein


Mass: 14583.515 Da / Num. of mol.: 5 / Fragment: UNP residues 1-126
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CEP170, FAM68A, KAB, KIAA0470, NM_001042404 / Plasmid: SGC / Production host: Escherichia Coli (E. coli) / References: UniProt: Q5SW79
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


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


Mass: 18.015 Da / Num. of mol.: 296 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsSEQUENCE THE CONSTRUCT WAS EXPRESSED WITH AN N-TERMINAL PURIFICATION TAG CONTAINING 6HIS-HA-FLAG- ...SEQUENCE THE CONSTRUCT WAS EXPRESSED WITH AN N-TERMINAL PURIFICATION TAG CONTAINING 6HIS-HA-FLAG-TEV SITES - MHHHHHHYPYDVPDYADYKDDDDKENLYFQS. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING ONLY A SER (0) FOLLOWED BY RESIDUES 1-126 OF THE TARGET SEQUENCE.

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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: 2.91 Å3/Da / Density % sol: 57.66 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 59% 2-methyl-2,4-pentanediol, 0.1M Bicine pH 8.0, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.97862
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 23, 2013
Details: Flat mirror (vertical focusing); single crystal Si(111) bent monochromator (horizontal focusing)
RadiationMonochromator: single crystal Si(111) bent / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97862 Å / Relative weight: 1
ReflectionResolution: 2.15→48.634 Å / Num. obs: 46447 / % possible obs: 99.6 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 38.33 Å2 / Rmerge(I) obs: 0.101 / Net I/σ(I): 14.07
Reflection shell

Rmerge(I) obs: 0.011 / Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Mean I/σ(I) obsNum. measured obsNum. unique obs% possible all
2.1-2.151.316077358497.7
2.15-2.211.820217352399.4
2.21-2.282.323841345399.9
2.28-2.352.823146337199.8
2.35-2.423.322085324999.8
2.42-2.513.720829314299.8
2.51-2.64.219419304499.8
2.6-2.71620538295999.8
2.71-2.838.3193022808100
2.83-2.9710.618239271099.9
2.97-3.131416162256899.9
3.13-3.3218.116573244499.9
3.32-3.552515754230499.9
3.55-3.8331.214336214299.8
3.83-4.236.312191196499.7
4.2-4.745.512495182499.9
4.7-5.4245.310577159499.9
5.42-6.6439.18308135699.7
6.64-9.3943.67027109199.9
9.3956.7349261697.5

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
MolProbity3beta29model building
PDB_EXTRACT3.1data extraction
PHASER2.3.0phasing
XSCALEJuly 4, 2012data scaling
BUSTER-TNT2.10.0refinement
XDSdata reduction
BUSTER2.10.0refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.15→48.634 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.937 / Occupancy max: 1 / Occupancy min: 0.4 / Cross valid method: THROUGHOUT / σ(F): 0
Details: 1. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS. 2. GOL MODELED IS PRESENT IN CRYSTALLIZATION/CRYO CONDITIONS. 3. NCS ...Details: 1. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS. 2. GOL MODELED IS PRESENT IN CRYSTALLIZATION/CRYO CONDITIONS. 3. NCS RESTRAINTS WERE APPLIED USING BUSTER'S LSSR RESTRAINT REPRESENTATION (-AUTONCS)
RfactorNum. reflection% reflectionSelection details
Rfree0.2029 2344 5.05 %RANDOM
Rwork0.1826 ---
obs0.1837 46411 99.8 %-
Displacement parametersBiso max: 151.27 Å2 / Biso mean: 50.5313 Å2 / Biso min: 21.3 Å2
Baniso -1Baniso -2Baniso -3
1--5.169 Å20 Å20 Å2
2--4.269 Å20 Å2
3---0.8999 Å2
Refine analyzeLuzzati coordinate error obs: 0.286 Å
Refinement stepCycle: LAST / Resolution: 2.15→48.634 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4877 0 6 296 5179
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d2375SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes141HARMONIC2
X-RAY DIFFRACTIONt_gen_planes711HARMONIC5
X-RAY DIFFRACTIONt_it4974HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion639SEMIHARMONIC5
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_contact5399SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d4974HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg6712HARMONIC21.07
X-RAY DIFFRACTIONt_omega_torsion3.88
X-RAY DIFFRACTIONt_other_torsion2.69
LS refinement shellResolution: 2.15→2.21 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2463 174 5.2 %
Rwork0.2199 3173 -
all0.2213 3347 -
obs--99.8 %
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)
11.02571.11270.11423.6576-0.20570.88980.0629-0.15170.110.3991-0.12250.0073-0.1035-0.09960.0596-0.006-0.02730.0305-0.0401-0.0055-0.088621.766825.914233.0053
21.04520.13270.03092.55770.97711.18190.06830.0112-0.04760.0569-0.13520.1957-0.0435-0.08990.067-0.0706-0.01020.019-0.0383-0.0147-0.011110.61536.275916.005
30.5649-0.75741.11112.6754-1.18032.80560.08980.2261-0.0491-0.0327-0.2287-0.21120.39780.54420.1389-0.10850.08030.0294-0.0180.0131-0.039129.3976-12.636310.8822
40.3435-0.10170.21183.9657-2.16524.71770.1661-0.0461-0.05660.2245-0.1666-0.04030.10880.39330.0006-0.07920.0254-0.0562-0.05580.0335-0.095332.274-27.178834.8481
53.93780.81421.21971.75481.39411.50590.0921-0.54420.54420.3347-0.45220.54420.0028-0.38620.3601-0.1918-0.01370.0744-0.1178-0.1520.083412.7969-47.567232.7314
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{A|1 - 122}A1 - 122
2X-RAY DIFFRACTION2{B|1 - 123}B1 - 123
3X-RAY DIFFRACTION3{C|1 - 118}C1 - 118
4X-RAY DIFFRACTION4{D|1 - 120}D1 - 120
5X-RAY DIFFRACTION5{E|0 - 121}E0 - 121

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