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Yorodumi- PDB-6lae: Crystal structure of the DNA-binding domain of human XPA in compl... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6lae | ||||||
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Title | Crystal structure of the DNA-binding domain of human XPA in complex with DNA | ||||||
Components |
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Keywords | DNA 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 factor 1 complex / nucleotide-excision repair involved in interstrand cross-link repair / 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 factor 1 complex / nucleotide-excision repair involved in interstrand cross-link repair / 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 / nucleus / metal ion binding Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.81 Å | ||||||
Authors | Lian, F.M. / Yang, X. / Jiang, Y.L. / Yang, F. / Li, C. / Yang, W. / Qian, C. | ||||||
Funding support | China, 1items
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Citation | Journal: 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6lae.cif.gz | 78.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6lae.ent.gz | 54.1 KB | Display | PDB format |
PDBx/mmJSON format | 6lae.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6lae_validation.pdf.gz | 975.1 KB | Display | wwPDB validaton report |
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Full document | 6lae_full_validation.pdf.gz | 987 KB | Display | |
Data in XML | 6lae_validation.xml.gz | 12.9 KB | Display | |
Data in CIF | 6lae_validation.cif.gz | 16.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/la/6lae ftp://data.pdbj.org/pub/pdb/validation_reports/la/6lae | HTTPS FTP |
-Related structure data
Related structure data | 6j44S S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: 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 | | Mass: 3285.148 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) #3: DNA chain | | Mass: 3414.234 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) #4: Chemical | #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.12 Å3/Da / Density % sol: 41.9 % |
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Crystal grow | Temperature: 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 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97775 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 24, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97775 Å / Relative weight: 1 |
Reflection twin | Operator: -h,-k,l / Fraction: 0.5 |
Reflection | Resolution: 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 shell | Resolution: 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 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 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
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 120 Å2 / Biso mean: 77.261 Å2 / Biso min: 30 Å2
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Refinement step | Cycle: final / Resolution: 2.81→43.7 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.81→2.881 Å / Rfactor Rfree error: 0
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