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Yorodumi- PDB-6j44: Crystal structure of the redefined DNA-binding domain of human XPA -
+Open data
-Basic information
Entry | Database: PDB / ID: 6j44 | ||||||
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Title | Crystal structure of the redefined DNA-binding domain of human XPA | ||||||
Components | DNA repair protein complementing XP-A cells | ||||||
Keywords | DNA BINDING PROTEIN / DNA repair / nucleotide excision repair / scaffold protein / zinc finger | ||||||
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 | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.06 Å | ||||||
Authors | Lian, F.M. / Yang, X. / Yang, W. / Jiang, Y.L. / Qian, C. | ||||||
Funding support | China, 1items
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Citation | Journal: Biochem.Biophys.Res.Commun. / Year: 2019 Title: Structural characterization of the redefined DNA-binding domain of human XPA. Authors: Lian, F.M. / Yang, X. / Yang, W. / Jiang, Y.L. / Qian, C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6j44.cif.gz | 41.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6j44.ent.gz | 27.4 KB | Display | PDB format |
PDBx/mmJSON format | 6j44.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/j4/6j44 ftp://data.pdbj.org/pub/pdb/validation_reports/j4/6j44 | HTTPS FTP |
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-Related structure data
Similar structure data |
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-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.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: XPA, XPAC / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta / References: UniProt: P23025 |
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#2: Chemical | ChemComp-ZN / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.83 Å3/Da / Density % sol: 56.58 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 1.8 M Ammonium citrate tribasic |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 1.2824 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: 1.2824 Å / Relative weight: 1 |
Reflection | Resolution: 2.06→50 Å / Num. obs: 10924 / % possible obs: 100 % / Redundancy: 9.9 % / Biso Wilson estimate: 43.6 Å2 / Rmerge(I) obs: 0.125 / Rpim(I) all: 0.041 / Rrim(I) all: 0.132 / Net I/σ(I): 16.1 |
Reflection shell | Resolution: 2.06→2.13 Å / Redundancy: 9.1 % / Rmerge(I) obs: 0.442 / Num. unique obs: 1077 / Rpim(I) all: 0.154 / Rrim(I) all: 0.468 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.06→35.46 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.939 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.182 / ESU R Free: 0.163 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 98.03 Å2 / Biso mean: 50.546 Å2 / Biso min: 32.78 Å2
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Refinement step | Cycle: final / Resolution: 2.06→35.46 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.064→2.118 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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