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- PDB-6lae: Crystal structure of the DNA-binding domain of human XPA in compl... -

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Basic information

Entry
Database: PDB / ID: 6lae
TitleCrystal structure of the DNA-binding domain of human XPA in complex with DNA
Components
  • DNA (5'-D(P*GP*CP*AP*TP*CP*TP*CP*GP*CP*CP*T)-3')
  • DNA (5'-D(P*TP*GP*GP*CP*GP*AP*GP*AP*TP*GP*C)-3')
  • DNA repair protein complementing XP-A cells
KeywordsDNA BINDING PROTEIN/DNA / Protein-DNA complex / nucleotide excision repair / DNA repair / DNA BINDING PROTEIN / DNA BINDING PROTEIN-DNA complex
Function / homology
Function and homology information


nucleotide-excision repair involved in interstrand cross-link repair / nucleotide-excision repair factor 1 complex / nucleotide-excision repair, DNA damage recognition / response to auditory stimulus / UV protection / UV-damage excision repair / intercellular bridge / protein localization to nucleus / nucleotide-excision repair / base-excision repair ...nucleotide-excision repair involved in interstrand cross-link repair / nucleotide-excision repair factor 1 complex / nucleotide-excision repair, DNA damage recognition / response to auditory stimulus / UV protection / UV-damage excision repair / intercellular bridge / protein localization to nucleus / nucleotide-excision repair / base-excision repair / Dual Incision in GG-NER / Formation of TC-NER Pre-Incision Complex / Formation of Incision Complex in GG-NER / Dual incision in TC-NER / sequence-specific double-stranded DNA binding / damaged DNA binding / protein domain specific binding / DNA repair / protein homodimerization activity / nucleoplasm / metal ion binding / nucleus
Similarity search - Function
XPA protein N-terminal / XPA / Zinc finger, XPA-type, conserved site / XPA, C-terminal / XPA, conserved site / XPA protein C-terminus / XPA protein signature 1. / XPA protein signature 2. / XPA domain superfamily / Putative DNA-binding domain superfamily
Similarity search - Domain/homology
DNA / DNA (> 10) / DNA repair protein complementing XP-A cells
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.81 Å
AuthorsLian, F.M. / Yang, X. / Jiang, Y.L. / Yang, F. / Li, C. / Yang, W. / Qian, C.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China31700672 China
CitationJournal: Int.J.Biol.Macromol. / Year: 2020
Title: New structural insights into the recognition of undamaged splayed-arm DNA with a single pair of non-complementary nucleotides by human nucleotide excision repair protein XPA.
Authors: Lian, F.M. / Yang, X. / Jiang, Y.L. / Yang, F. / Li, C. / Yang, W. / Qian, C.
History
DepositionNov 12, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 26, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 22, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DNA repair protein complementing XP-A cells
B: DNA repair protein complementing XP-A cells
C: DNA (5'-D(P*GP*CP*AP*TP*CP*TP*CP*GP*CP*CP*T)-3')
D: DNA (5'-D(P*TP*GP*GP*CP*GP*AP*GP*AP*TP*GP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,7776
Polymers41,6464
Non-polymers1312
Water1086
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3300 Å2
ΔGint-16 kcal/mol
Surface area19260 Å2
Unit cell
Length a, b, c (Å)69.112, 69.112, 63.938
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number144
Space group name H-MP31

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Components

#1: Protein DNA repair protein complementing XP-A cells / / Xeroderma pigmentosum group A-complementing protein


Mass: 17473.172 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: XPA, XPAC / Production host: Escherichia coli (E. coli) / References: UniProt: P23025
#2: DNA chain DNA (5'-D(P*GP*CP*AP*TP*CP*TP*CP*GP*CP*CP*T)-3')


Mass: 3285.148 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#3: DNA chain DNA (5'-D(P*TP*GP*GP*CP*GP*AP*GP*AP*TP*GP*C)-3')


Mass: 3414.234 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.12 Å3/Da / Density % sol: 41.9 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: 20% PEG4000, 20% 2-propanol, 0.1 mM sodium citrate tribasic pH 5.6

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97775 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 24, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97775 Å / Relative weight: 1
Reflection twinOperator: -h,-k,l / Fraction: 0.5
ReflectionResolution: 2.8→50 Å / Num. obs: 7795 / % possible obs: 93.2 % / Redundancy: 4.1 % / Biso Wilson estimate: 68.3 Å2 / Rmerge(I) obs: 0.104 / Rpim(I) all: 0.056 / Rrim(I) all: 0.119 / Net I/σ(I): 10.2
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.495 / Num. unique obs: 778 / Rpim(I) all: 0.259 / Rrim(I) all: 0.562 / % possible all: 92.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0257refinement
HKL-2000data scaling
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6J44

6j44


Resolution: 2.81→43.7 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.929 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.084 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2369 459 5.9 %RANDOM
Rwork0.2185 ---
obs0.2198 7335 93.37 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 120 Å2 / Biso mean: 77.261 Å2 / Biso min: 30 Å2
Baniso -1Baniso -2Baniso -3
1-18.6 Å20 Å20 Å2
2--18.6 Å20 Å2
3----37.2 Å2
Refinement stepCycle: final / Resolution: 2.81→43.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1940 450 2 6 2398
Biso mean--75.94 30 -
Num. residues----254
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0122478
X-RAY DIFFRACTIONr_bond_other_d0.0320.0182091
X-RAY DIFFRACTIONr_angle_refined_deg1.7011.5443414
X-RAY DIFFRACTIONr_angle_other_deg2.3161.7654917
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.4095230
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.30524.211114
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.81815414
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.7881510
X-RAY DIFFRACTIONr_chiral_restr0.0940.2306
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.022408
X-RAY DIFFRACTIONr_gen_planes_other0.0140.02486
LS refinement shellResolution: 2.81→2.881 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.458 37 -
Rwork0.449 534 -
obs--92.69 %

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