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- PDB-4pxw: Crystal structure of human DCAF1 WD40 repeats (Q1250L) -

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Basic information

Entry
Database: PDB / ID: 4pxw
TitleCrystal structure of human DCAF1 WD40 repeats (Q1250L)
ComponentsProtein VPRBP
KeywordsTRANSFERASE / structural genomics / Structural Genomics Consortium / SGC
Function / homology
Function and homology information


histone H2AT120 kinase activity / cell competition in a multicellular organism / V(D)J recombination / Cul4-RING E3 ubiquitin ligase complex / ubiquitin-like ligase-substrate adaptor activity / B cell differentiation / post-translational protein modification / nuclear estrogen receptor binding / fibrillar center / positive regulation of protein catabolic process ...histone H2AT120 kinase activity / cell competition in a multicellular organism / V(D)J recombination / Cul4-RING E3 ubiquitin ligase complex / ubiquitin-like ligase-substrate adaptor activity / B cell differentiation / post-translational protein modification / nuclear estrogen receptor binding / fibrillar center / positive regulation of protein catabolic process / Antigen processing: Ubiquitination & Proteasome degradation / non-specific serine/threonine protein kinase / protein ubiquitination / phosphorylation / protein serine kinase activity / negative regulation of transcription by RNA polymerase II / nucleoplasm / ATP binding / nucleus / cytoplasm
Similarity search - Function
VPRBP/DCAF1 family / Lissencephaly type-1-like homology motif / LIS1 homology (LisH) motif profile. / LIS1 homology motif / YVTN repeat-like/Quinoprotein amine dehydrogenase / 7 Propeller / Methylamine Dehydrogenase; Chain H / Armadillo-like helical / Armadillo-type fold / WD40-repeat-containing domain superfamily ...VPRBP/DCAF1 family / Lissencephaly type-1-like homology motif / LIS1 homology (LisH) motif profile. / LIS1 homology motif / YVTN repeat-like/Quinoprotein amine dehydrogenase / 7 Propeller / Methylamine Dehydrogenase; Chain H / Armadillo-like helical / Armadillo-type fold / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily / Mainly Beta
Similarity search - Domain/homology
DDB1- and CUL4-associated factor 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.72 Å
AuthorsXu, C. / Tempel, W. / He, H. / Li, Y. / Walker, J.R. / Bountra, C. / Arrowsmith, C.H. / Edwards, A.M. / Min, J. / Structural Genomics Consortium (SGC)
CitationJournal: TO BE PUBLISHED
Title: Crystal structure of human DCAF1 WD40 repeats (Q1250L)
Authors: Xu, C. / Tempel, W. / He, H. / Seitova, A. / Li, Y. / Walker, J.R. / Bountra, C. / Arrowsmith, C.H. / Edwards, A.M. / Min, J. / Structural Genomics Consortium (SGC)
History
DepositionMar 25, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 16, 2014Provider: repository / Type: Initial release
Revision 1.1May 10, 2017Group: Other / Structure summary
Revision 1.2Sep 20, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Protein VPRBP
B: Protein VPRBP


Theoretical massNumber of molelcules
Total (without water)87,27447
Polymers87,2742
Non-polymers045
Water7,440413
1
A: Protein VPRBP


Theoretical massNumber of molelcules
Total (without water)43,63723
Polymers43,6371
Non-polymers022
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Protein VPRBP


Theoretical massNumber of molelcules
Total (without water)43,63724
Polymers43,6371
Non-polymers023
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)74.888, 99.422, 84.900
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
DetailsAUTHORS HAVE INDICATED THAT THE BIOLOGICAL UNIT IS UNKNOWN

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Components

#1: Protein Protein VPRBP / DDB1- and CUL4-associated factor 1 / HIV-1 Vpr-binding protein / VprBP / Serine/threonine-protein ...DDB1- and CUL4-associated factor 1 / HIV-1 Vpr-binding protein / VprBP / Serine/threonine-protein kinase VPRBP / Vpr-interacting protein


Mass: 43636.852 Da / Num. of mol.: 2 / Mutation: Q1250L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: VPRBP, DCAF1, KIAA0800, RIP / Plasmid: pFBOH-MHL / Cell line (production host): sf9 / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: Q9Y4B6, non-specific serine/threonine protein kinase
#2: Chemical...
ChemComp-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 45 / Source method: obtained synthetically
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 413 / 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: 1.81 Å3/Da / Density % sol: 32.07 %
Crystal growTemperature: 291 K / Method: vapor diffusion / pH: 7.5
Details: 0.1 M sodium hepes, 0.2 M lithium sulfate, 25% PEG3350, pH 7.5, VAPOR DIFFUSION, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97856 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 10, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 1.72→48.9 Å / Num. obs: 67989 / % possible obs: 100 % / Redundancy: 7.3 % / Rmerge(I) obs: 0.131 / Net I/σ(I): 11.4
Reflection shell

Rmerge(I) obs: 0.012 / Diffraction-ID: 1

Resolution (Å)Redundancy (%)Mean I/σ(I) obsNum. measured allNum. unique all% possible all
1.72-1.757.41.926202355599.8
9.1-48.96.133331554199

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
Aimless0.2.17data scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACT3.14data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 4cc9

4cc9


Resolution: 1.72→48 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.95 / WRfactor Rfree: 0.1868 / WRfactor Rwork: 0.1532 / Occupancy max: 1 / Occupancy min: 0.3 / FOM work R set: 0.7591 / SU B: 2.906 / SU ML: 0.09 / SU R Cruickshank DPI: 0.1075 / SU Rfree: 0.1066 / Cross valid method: THROUGHOUT / ESU R: 0.107 / ESU R Free: 0.107 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: Arp/warp was used for automated model building. COOT was used for interactive model building. Model geometry was evaluated with MOLPROBITY.
RfactorNum. reflection% reflectionSelection details
Rfree0.2189 2264 3.3 %RANDOM
Rwork0.1828 ---
obs0.184 67936 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 max: 75.84 Å2 / Biso mean: 17.9421 Å2 / Biso min: 7.99 Å2
Baniso -1Baniso -2Baniso -3
1-1.92 Å20 Å2-0 Å2
2---1.25 Å20 Å2
3----0.67 Å2
Refinement stepCycle: LAST / Resolution: 1.72→48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4609 0 45 413 5067
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0194807
X-RAY DIFFRACTIONr_bond_other_d0.0010.024391
X-RAY DIFFRACTIONr_angle_refined_deg1.6831.9276539
X-RAY DIFFRACTIONr_angle_other_deg0.861310069
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0935598
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.04823.933239
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.0215775
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.7621528
X-RAY DIFFRACTIONr_chiral_restr0.1140.2730
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.025527
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021205
X-RAY DIFFRACTIONr_mcbond_it2.0541.5262354
X-RAY DIFFRACTIONr_mcbond_other2.051.5252353
X-RAY DIFFRACTIONr_mcangle_it2.9712.2742939
LS refinement shellResolution: 1.72→1.765 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.299 243 -
Rwork0.287 4715 -
all-4958 -
obs--99.78 %

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