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- PDB-7kyq: Crystal structure of human BCCIP beta (Native1) -

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Basic information

Entry
Database: PDB / ID: 7kyq
TitleCrystal structure of human BCCIP beta (Native1)
ComponentsBRCA2 and CDKN1A-interacting protein
KeywordsTRANSFERASE / BRCA2 / eIF6 / cancer suppressor / ribosome biogenesis / GNAT / GCN5-related acetyltransferase
Function / homology
Function and homology information


nuclear cyclin-dependent protein kinase holoenzyme complex / microtubule anchoring / neuroendocrine cell differentiation / kinase regulator activity / regulation of cyclin-dependent protein serine/threonine kinase activity / mitotic spindle pole / establishment of mitotic spindle orientation / mitotic spindle assembly / centriole / tubulin binding ...nuclear cyclin-dependent protein kinase holoenzyme complex / microtubule anchoring / neuroendocrine cell differentiation / kinase regulator activity / regulation of cyclin-dependent protein serine/threonine kinase activity / mitotic spindle pole / establishment of mitotic spindle orientation / mitotic spindle assembly / centriole / tubulin binding / mitotic spindle organization / microtubule cytoskeleton organization / DNA repair / centrosome / RNA binding / nucleoplasm / nucleus / cytosol
Similarity search - Function
BRCA2 and CDKN1A-interacting protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3.06 Å
AuthorsChoi, W.S. / Liu, B. / Shen, Z. / Yang, W.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)DK036146 United States
CitationJournal: Protein Sci. / Year: 2021
Title: Structure of human BCCIP and implications for binding and modification of partner proteins.
Authors: Choi, W.S. / Liu, B. / Shen, Z. / Yang, W.
History
DepositionDec 8, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 9, 2021Provider: repository / Type: Initial release
Revision 1.1Mar 6, 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: BRCA2 and CDKN1A-interacting protein


Theoretical massNumber of molelcules
Total (without water)29,2831
Polymers29,2831
Non-polymers00
Water79344
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area12200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)112.670, 112.670, 56.360
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Space group name HallP4abw2nw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+1/4
#3: y+1/2,-x+1/2,z+3/4
#4: x+1/2,-y+1/2,-z+3/4
#5: -x+1/2,y+1/2,-z+1/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2
Components on special symmetry positions
IDModelComponents
11A-439-

HOH

21A-443-

HOH

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Components

#1: Protein BRCA2 and CDKN1A-interacting protein / P21- and CDK-associated protein 1 / Protein TOK-1


Mass: 29282.535 Da / Num. of mol.: 1 / Fragment: UNP residues 61-314
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BCCIP, TOK1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9P287, Transferases
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 44 / 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: 3.08 Å3/Da / Density % sol: 60.05 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / Details: 0.2 M tri-sodium citrate, 18-20% PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Aug 17, 2019
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.04→40 Å / Num. obs: 7295 / % possible obs: 99.8 % / Redundancy: 12.4 % / Biso Wilson estimate: 85.03 Å2 / CC1/2: 0.995 / Net I/σ(I): 12.4
Reflection shellResolution: 3.04→3.09 Å / Mean I/σ(I) obs: 2.3 / Num. unique obs: 341 / CC1/2: 0.911

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
XDSdata reduction
XSCALEdata scaling
AutoSolphasing
RefinementMethod to determine structure: SAD / Resolution: 3.06→39.84 Å / SU ML: 0.3649 / Cross valid method: FREE R-VALUE / σ(F): 1.39 / Phase error: 27.1879
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2507 367 5.34 %
Rwork0.2173 6510 -
obs0.2191 6877 95.08 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 86.81 Å2
Refinement stepCycle: LAST / Resolution: 3.06→39.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1850 0 0 44 1894
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01311883
X-RAY DIFFRACTIONf_angle_d1.53912538
X-RAY DIFFRACTIONf_chiral_restr0.073287
X-RAY DIFFRACTIONf_plane_restr0.0074325
X-RAY DIFFRACTIONf_dihedral_angle_d19.0629712
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.06-3.50.29971000.27481899X-RAY DIFFRACTION85.14
3.51-4.410.29621310.23512240X-RAY DIFFRACTION100
4.42-39.840.221360.19462371X-RAY DIFFRACTION99.72
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)
16.90434905744-0.54106837899-2.913258729897.78354761031-0.2089624553544.304002903620.5265004122240.1753808587721.15260772122-0.225764085828-0.200295203358-1.30133853431-0.8683100447030.246375557566-5.92643777397E-80.6429606151070.04900253751660.1693701930230.633544807330.1434849454630.89683582440555.537385030737.14933290221.1692393759
22.76536374028-0.547767680764-0.4110501262423.426520927341.415976971970.258727497680.7709766322181.149740959670.145269631183-1.69117310355-0.660369411511-0.766254992011-0.4944883657190.273356022961-4.84825463733E-81.263674711970.4127608686940.330054994921.082843609550.1965577242210.81383703808155.028243664233.23019705347.61657777456
34.784500825353.37507136856-0.7279492287390.531867225014.105502364984.225781498350.3220192176361.197296826350.176239532876-1.00296718659-0.496176927915-0.102859731834-0.675022031316-0.3598780574360.0002716093595830.7726437057430.2129853050020.197873379690.9275598867610.1337086699990.57778656073946.70515777429.936207703614.6146411958
42.56260494286-2.91529014641-6.23005452922-0.1264312774811.529636915740.4128751525910.4261851531620.292807030366-0.940272457246-0.335938743623-0.2877879055940.0223229548647-0.039340451858-1.03245503523-9.99595272833E-90.874954643148-0.003740780817290.08714783629660.96772980759-0.02323844143281.0159466772858.567482491621.895724167812.0417445699
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A

IDRefine TLS-IDSelection detailsAuth seq-IDLabel seq-ID
11chain 'A' and (resid 59 through 157 )59 - 1571 - 89
22chain 'A' and (resid 158 through 188 )158 - 18890 - 120
33chain 'A' and (resid 189 through 253 )189 - 253121 - 169
44chain 'A' and (resid 254 through 314 )254 - 314170 - 230

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