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Yorodumi- PDB-3klw: Crystal structure of primosomal replication protein n from Bordet... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3klw | |||||||||
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Title | Crystal structure of primosomal replication protein n from Bordetella pertussis. northeast structural genomics consortium target ber132. | |||||||||
Components | Primosomal replication protein n | |||||||||
Keywords | DNA BINDING PROTEIN / STRUCTURAL GENOMICS / PSI-2 / PROTEIN STRUCTURE INITIATIVE / NORTHEAST STRUCTURAL GENOMICS CONSORTIUM / NESG / DNA REPLICATION / DNA-BINDING / PRIMOSOME | |||||||||
Function / homology | Function and homology information primosome complex / DNA replication, synthesis of primer / single-stranded DNA binding Similarity search - Function | |||||||||
Biological species | Bordetella pertussis (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2 Å | |||||||||
Authors | Kuzin, A.P. / Neely, H. / Vorobiev, S.M. / Seetharaman, J. / Forouhar, F. / Wang, H. / Janjua, H. / Maglaqui, M. / Xiao, T. / Liu, J. ...Kuzin, A.P. / Neely, H. / Vorobiev, S.M. / Seetharaman, J. / Forouhar, F. / Wang, H. / Janjua, H. / Maglaqui, M. / Xiao, T. / Liu, J. / Baran, M.C. / 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 primosomal replication protein n from Bordetella pertussis. northeast structural genomics consortium target ber132. Authors: Kuzin, A.P. / Neely, H. / Vorobiev, S.M. / Seetharaman, J. / Forouhar, F. / Wang, H. / Janjua, H. / Maglaqui, M. / Xiao, T. / Liu, J. / Baran, M.C. / Acton, T.B. / Rost, B. / Montelione, G.T. ...Authors: Kuzin, A.P. / Neely, H. / Vorobiev, S.M. / Seetharaman, J. / Forouhar, F. / Wang, H. / Janjua, H. / Maglaqui, M. / Xiao, T. / Liu, J. / Baran, M.C. / 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 | 3klw.cif.gz | 43.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3klw.ent.gz | 34.5 KB | Display | PDB format |
PDBx/mmJSON format | 3klw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kl/3klw ftp://data.pdbj.org/pub/pdb/validation_reports/kl/3klw | HTTPS FTP |
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-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: 10665.988 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bordetella pertussis (bacteria) / Gene: priB, BP2795 / References: UniProt: P67673 #2: Water | ChemComp-HOH / | |
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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: 2.87 Å3/Da / Density % sol: 57.15 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop Details: 0.1M Li2SO4, 0.1M Na citrate, 20% PEG8000, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.979 Å |
Detector | Type: MARMOSAIC 325 mm CCD / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 2→30 Å / Num. obs: 27094 / Observed criterion σ(I): -3 / Biso Wilson estimate: 13.5 Å2 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2→19.97 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 149384.84 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 63.2651 Å2 / ksol: 0.4 e/Å3 | ||||||||||||||||||||
Displacement parameters | Biso mean: 40.5 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2→19.97 Å
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Refine LS restraints |
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Refine LS restraints NCS | NCS model details: NONE | ||||||||||||||||||||
LS refinement shell | Resolution: 2→2.13 Å / Rfactor Rfree error: 0.014 / Total num. of bins used: 6
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Xplor file |
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