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Yorodumi- PDB-3e0e: Crystal structure of a domain of replication protein A from Metha... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3e0e | ||||||
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Title | Crystal structure of a domain of replication protein A from Methanococcus maripaludis. NorthEast Structural Genomics targe MrR110B | ||||||
Components | Replication protein A | ||||||
Keywords | REPLICATION / Replication protein A / Structural Genomics / PSI-2 / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG | ||||||
Function / homology | Function and homology information response to ionizing radiation / double-strand break repair via homologous recombination / DNA binding Similarity search - Function | ||||||
Biological species | Methanococcus maripaludis (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.6 Å | ||||||
Authors | Seetharaman, J. / Chen, Y. / Wang, H. / Janjua, H. / Foote, E.L. / Xiao, R. / Nair, R. / Everett, J.K. / Acton, T.B. / Rost, B. ...Seetharaman, J. / Chen, Y. / Wang, H. / Janjua, H. / Foote, E.L. / Xiao, R. / Nair, R. / Everett, J.K. / Acton, T.B. / Rost, B. / Montelione, G.T. / Hunt, J.F. / Tong, L. / Northeast Structural Genomics Consortium (NESG) | ||||||
Citation | Journal: To be Published Title: Crystal structure of a domain of replication protein A from Methanococcus maripaludis. NorthEast Structural Genomics targe MrR110B Authors: Seetharaman, J. / Chen, Y. / Wang, H. / Janjua, H. / Foote, E.L. / Xiao, R. / Nair, R. / Everett, J.K. / Acton, T.B. / Rost, B. / Montelione, G.T. / Hunt, J.F. / Tong, L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3e0e.cif.gz | 28.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3e0e.ent.gz | 20.7 KB | Display | PDB format |
PDBx/mmJSON format | 3e0e.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3e0e_validation.pdf.gz | 423 KB | Display | wwPDB validaton report |
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Full document | 3e0e_full_validation.pdf.gz | 424.5 KB | Display | |
Data in XML | 3e0e_validation.xml.gz | 7 KB | Display | |
Data in CIF | 3e0e_validation.cif.gz | 9.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/e0/3e0e ftp://data.pdbj.org/pub/pdb/validation_reports/e0/3e0e | HTTPS FTP |
-Related structure data
Similar structure data | |
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Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 10796.943 Da / Num. of mol.: 1 / Fragment: residues 173-267 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Methanococcus maripaludis (archaea) / Gene: rpa, MMP1032 / Plasmid: PET 21 / Production host: Escherichia coli (E. coli) / References: UniProt: Q6LYF9 |
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#2: 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: 1.81 Å3/Da / Density % sol: 31.87 % |
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Crystal grow | Temperature: 293 K / pH: 5 Details: Sodium chloride 0.1 M, Sodium Acetate 0.1 M, PEG 4000 40%, pH 5, Micro batch under oil method, temperature 293K |
-Data collection
Diffraction |
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Diffraction source |
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Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Jun 29, 2008 / Details: Mirrors | |||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 | |||||||||||||||
Reflection | Resolution: 1.6→50 Å / Num. obs: 19963 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 21.4 % / Biso Wilson estimate: 17.5 Å2 / Rmerge(I) obs: 0.048 / Rsym value: 0.044 | |||||||||||||||
Reflection shell | Resolution: 1.6→1.66 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.225 / Mean I/σ(I) obs: 19.5 / Num. unique all: 1987 / Rsym value: 0.213 / % possible all: 98.7 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.6→39.28 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 146558 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 61.0129 Å2 / ksol: 0.4 e/Å3 | ||||||||||||||||||||
Displacement parameters | Biso mean: 18.2 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.6→39.28 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.6→1.7 Å / Rfactor Rfree error: 0.02 / Total num. of bins used: 6
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Xplor file |
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