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- PDB-3e0c: Crystal Structure of DNA Damage-Binding protein 1(DDB1) -

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Basic information

Entry
Database: PDB / ID: 3e0c
TitleCrystal Structure of DNA Damage-Binding protein 1(DDB1)
ComponentsDNA damage-binding protein 1
KeywordsDNA BINDING PROTEIN / DNA DAMAGE-BINDING PROTEIN 1 / DDB1 / Structural Genomics / Structural Genomics Consortium / SGC / DNA damage / DNA repair / DNA-binding / Host-virus interaction / Nucleus / Phosphoprotein / Ubl conjugation pathway
Function / homology
Function and homology information


positive regulation by virus of viral protein levels in host cell / spindle assembly involved in female meiosis / epigenetic programming in the zygotic pronuclei / Cul4-RING E3 ubiquitin ligase complex / UV-damage excision repair / biological process involved in interaction with symbiont / regulation of mitotic cell cycle phase transition / WD40-repeat domain binding / Cul4A-RING E3 ubiquitin ligase complex / Cul4B-RING E3 ubiquitin ligase complex ...positive regulation by virus of viral protein levels in host cell / spindle assembly involved in female meiosis / epigenetic programming in the zygotic pronuclei / Cul4-RING E3 ubiquitin ligase complex / UV-damage excision repair / biological process involved in interaction with symbiont / regulation of mitotic cell cycle phase transition / WD40-repeat domain binding / Cul4A-RING E3 ubiquitin ligase complex / Cul4B-RING E3 ubiquitin ligase complex / ubiquitin ligase complex scaffold activity / negative regulation of reproductive process / negative regulation of developmental process / viral release from host cell / cullin family protein binding / ectopic germ cell programmed cell death / positive regulation of viral genome replication / proteasomal protein catabolic process / positive regulation of gluconeogenesis / nucleotide-excision repair / Recognition of DNA damage by PCNA-containing replication complex / regulation of circadian rhythm / DNA Damage Recognition in GG-NER / Transcription-Coupled Nucleotide Excision Repair (TC-NER) / Formation of TC-NER Pre-Incision Complex / Dual Incision in GG-NER / Wnt signaling pathway / Formation of Incision Complex in GG-NER / Dual incision in TC-NER / Gap-filling DNA repair synthesis and ligation in TC-NER / positive regulation of protein catabolic process / cellular response to UV / rhythmic process / site of double-strand break / Neddylation / protein-macromolecule adaptor activity / ubiquitin-dependent protein catabolic process / proteasome-mediated ubiquitin-dependent protein catabolic process / damaged DNA binding / chromosome, telomeric region / protein ubiquitination / DNA repair / DNA damage response / protein-containing complex binding / negative regulation of apoptotic process / nucleolus / apoptotic process / protein-containing complex / DNA binding / extracellular space / extracellular exosome / nucleoplasm / nucleus / cytoplasm
Similarity search - Function
DNA polymerase; domain 1 - #910 / Cleavage/polyadenylation specificity factor, A subunit, N-terminal / Mono-functional DNA-alkylating methyl methanesulfonate N-term / Cleavage/polyadenylation specificity factor, A subunit, C-terminal / : / CPSF A subunit region / YVTN repeat-like/Quinoprotein amine dehydrogenase / 7 Propeller / Methylamine Dehydrogenase; Chain H / DNA polymerase; domain 1 ...DNA polymerase; domain 1 - #910 / Cleavage/polyadenylation specificity factor, A subunit, N-terminal / Mono-functional DNA-alkylating methyl methanesulfonate N-term / Cleavage/polyadenylation specificity factor, A subunit, C-terminal / : / CPSF A subunit region / YVTN repeat-like/Quinoprotein amine dehydrogenase / 7 Propeller / Methylamine Dehydrogenase; Chain H / DNA polymerase; domain 1 / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
DNA damage-binding protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.41 Å
AuthorsAmaya, M.F. / Xu, L. / Hao, H. / Bountra, C. / Wickstroem, M. / Arrowsmith, C.H. / Edwards, A.M. / Bochkarev, A. / Min, J. / Structural Genomics Consortium (SGC)
CitationJournal: Protein Cell / Year: 2011
Title: Structure and function of WD40 domain proteins.
Authors: Xu, C. / Min, J.
History
DepositionJul 31, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 16, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.3Aug 30, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DNA damage-binding protein 1


Theoretical massNumber of molelcules
Total (without water)127,0971
Polymers127,0971
Non-polymers00
Water3,369187
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)62.607, 124.153, 167.822
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein DNA damage-binding protein 1 / Damage-specific DNA-binding protein 1 / UV-damaged DNA-binding factor / DDB p127 subunit / DNA ...Damage-specific DNA-binding protein 1 / UV-damaged DNA-binding factor / DDB p127 subunit / DNA damage-binding protein a / DDBa / UV-damaged DNA-binding protein 1 / UV-DDB 1 / Xeroderma pigmentosum group E-complementing protein / XPCe / XPE-binding factor / XPE-BF / HBV X-associated protein 1 / XAP-1


Mass: 127097.469 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DDB1, XAP1 / Production host: Baculovirus / References: UniProt: Q16531
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 187 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.57 Å3/Da / Density % sol: 52.06 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1 M Bis tris, pH 6.5,0.2 M Lithium sulfate, 25% PEG 3350, 1:6000 Protein:Chymotrypsin , VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97935 Å
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97935 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. obs: 51628 / % possible obs: 100 % / Redundancy: 7.3 % / Rmerge(I) obs: 0.091 / Χ2: 1.212
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
2.4-2.447.30.90325230.922100
2.44-2.497.40.8425550.954100
2.49-2.537.40.78325161.019100
2.53-2.597.40.64925690.949100
2.59-2.647.40.53825290.951100
2.64-2.77.40.45725741.043100
2.7-2.777.40.36925141100
2.77-2.857.40.29625761.006100
2.85-2.937.40.2425531.031100
2.93-3.027.40.1925511.055100
3.02-3.137.40.15525681.1100
3.13-3.267.40.11725581.148100
3.26-3.417.40.09325651.21100
3.41-3.587.30.07925801.32100
3.58-3.817.30.06825911.358100
3.81-4.17.30.06226021.474100
4.1-4.527.20.06126142.036100
4.52-5.177.10.05926342.367100
5.17-6.516.90.0526461.425100
6.51-506.80.02628100.88399.9

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.2.0019refinement
PDB_EXTRACT3.006data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2B5M

2b5m


Resolution: 2.41→49.88 Å / Cor.coef. Fo:Fc: 0.929 / Cor.coef. Fo:Fc free: 0.893 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 16.809 / SU ML: 0.199 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.363 / ESU R Free: 0.276 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.283 2623 5.1 %RANDOM
Rwork0.224 ---
obs0.227 51552 99.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 196.35 Å2 / Biso mean: 24.249 Å2 / Biso min: 2.15 Å2
Baniso -1Baniso -2Baniso -3
1--0.68 Å20 Å20 Å2
2--1.52 Å20 Å2
3----0.84 Å2
Refinement stepCycle: LAST / Resolution: 2.41→49.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7545 0 0 187 7732
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0227718
X-RAY DIFFRACTIONr_angle_refined_deg1.5171.96310492
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.9265993
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.59524.367300
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.222151196
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.5511531
X-RAY DIFFRACTIONr_chiral_restr0.0940.21268
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.025707
X-RAY DIFFRACTIONr_nbd_refined0.2050.22880
X-RAY DIFFRACTIONr_nbtor_refined0.3020.25121
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1510.2365
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1830.225
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2170.24
X-RAY DIFFRACTIONr_mcbond_it0.7641.55164
X-RAY DIFFRACTIONr_mcangle_it1.33528023
X-RAY DIFFRACTIONr_scbond_it1.86132888
X-RAY DIFFRACTIONr_scangle_it2.8564.52469
LS refinement shellResolution: 2.405→2.468 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.378 199 -
Rwork0.282 3408 -
all-3607 -
obs--96.32 %

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