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Yorodumi- PDB-1d4u: INTERACTIONS OF HUMAN NUCLEOTIDE EXCISION REPAIR PROTEIN XPA WITH... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1d4u | ||||||
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Title | INTERACTIONS OF HUMAN NUCLEOTIDE EXCISION REPAIR PROTEIN XPA WITH RPA70 AND DNA: CHEMICAL SHIFT MAPPING AND 15N NMR RELAXATION STUDIES | ||||||
Components | NUCLEOTIDE EXCISION REPAIR PROTEIN XPA (XPA-MBD) | ||||||
Keywords | DNA BINDING PROTEIN / DNA REPAIR / LOOP-RICH DOMAIN / NMR RELAXATION | ||||||
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 / Formation of TC-NER Pre-Incision Complex / Dual Incision in GG-NER / 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 | SOLUTION NMR / simulated annealing | ||||||
Authors | Buchko, G.W. / Daughdrill, G.W. / de Lorimier, R. / Rao, S. / Isern, N.G. / Lingbeck, J. / Taylor, J. / Wold, M.S. / Gochin, M. / Spicer, L.D. ...Buchko, G.W. / Daughdrill, G.W. / de Lorimier, R. / Rao, S. / Isern, N.G. / Lingbeck, J. / Taylor, J. / Wold, M.S. / Gochin, M. / Spicer, L.D. / Lowry, D.F. / Kennedy, M.A. | ||||||
Citation | Journal: Biochemistry / Year: 1999 Title: Interactions of human nucleotide excision repair protein XPA with DNA and RPA70 Delta C327: chemical shift mapping and 15N NMR relaxation studies. Authors: Buchko, G.W. / Daughdrill, G.W. / de Lorimier, R. / Rao B, K. / Isern, N.G. / Lingbeck, J.M. / Taylor, J.S. / Wold, M.S. / Gochin, M. / Spicer, L.D. / Lowry, D.F. / Kennedy, M.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1d4u.cif.gz | 48.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1d4u.ent.gz | 34.2 KB | Display | PDB format |
PDBx/mmJSON format | 1d4u.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1d4u_validation.pdf.gz | 292.5 KB | Display | wwPDB validaton report |
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Full document | 1d4u_full_validation.pdf.gz | 292.3 KB | Display | |
Data in XML | 1d4u_validation.xml.gz | 6 KB | Display | |
Data in CIF | 1d4u_validation.cif.gz | 7.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/d4/1d4u ftp://data.pdbj.org/pub/pdb/validation_reports/d4/1d4u | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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NMR ensembles |
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-Components
#1: Protein | Mass: 13278.207 Da / Num. of mol.: 1 / Fragment: XPA-MBD Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: P23025 |
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#2: Chemical | ChemComp-ZN / |
-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||||||||||||||
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NMR experiment |
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NMR details | Text: 3D NOESY AND TOCSY SPECTRA WERE COLLECTED ON THE CO2+ SUBSTITUTED XPA-MBD. |
-Sample preparation
Details | Contents: 50MM TRIS-HCL;PH7.3,150MM KCL, 25MM DTT |
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Sample conditions | Ionic strength: 150mM / pH: 7.3 / Pressure: 1ATM. / Temperature: 303 K |
Crystal grow | *PLUS Method: other / Details: NMR |
-NMR measurement
NMR spectrometer |
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-Processing
NMR software | Name: X-PLOR / Version: 3.1 / Developer: BRUNGER, A.T. / Classification: refinement |
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Refinement | Method: simulated annealing / Software ordinal: 1 Details: PARAMAGNETIC PSEUDOCONTACT SHIFTS WERE USED IN THE REFINEMENT. |
NMR representative | Selection criteria: lowest energy |
NMR ensemble | Conformer selection criteria: structures with the least restraint violations Conformers calculated total number: 10 / Conformers submitted total number: 1 |