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Yorodumi- PDB-1rzn: Crystal Structure of Penicillin-binding protein-related factor A ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1rzn | ||||||
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Title | Crystal Structure of Penicillin-binding protein-related factor A from Bacillus Subtilis. | ||||||
Components | Recombination protein UGenetic recombination | ||||||
Keywords | DNA BINDING PROTEIN / DNA repair / DNA recombination / Structural Genomics / PSI / Protein Structure Initiative / New York SGX Research Center for Structural Genomics / NYSGXRC | ||||||
Function / homology | Function and homology information crossover junction endodeoxyribonuclease / chromosome segregation / endonuclease activity / DNA recombination / DNA repair / magnesium ion binding / DNA binding / cytoplasm Similarity search - Function | ||||||
Biological species | Bacillus subtilis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 2.302 Å | ||||||
Authors | Ramagopal, U.A. / Almo, S.C. / Burley, S.K. / New York SGX Research Center for Structural Genomics (NYSGXRC) | ||||||
Citation | Journal: To be Published Title: Crystal Structure of Penicillin-binding protein-related factor A from Bacillus Subtilis. Authors: Ramagopal, U.A. / Almo, S.C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1rzn.cif.gz | 76.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1rzn.ent.gz | 58.4 KB | Display | PDB format |
PDBx/mmJSON format | 1rzn.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rz/1rzn ftp://data.pdbj.org/pub/pdb/validation_reports/rz/1rzn | 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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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Ens-ID: 1 / Refine code: 5
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-Components
#1: Protein | Mass: 23863.912 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: RECU, PRFA, BSU22310 / Production host: Escherichia coli (E. coli) / References: UniProt: P39792 #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 2 |
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-Sample preparation
Crystal | Density Matthews: 2.6 Å3/Da / Density % sol: 52.72 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: PEG 8000, Tris/HCl, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction |
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Diffraction source |
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Detector |
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Radiation | Monochromator: Double crystal SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||
Radiation wavelength |
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Reflection | Resolution: 2.302→30 Å / Num. all: 17965 / Num. obs: 17965 / % possible obs: 98.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 8.5 % / Biso Wilson estimate: 42.4 Å2 / Rmerge(I) obs: 0.086 / Net I/σ(I): 21.4 |
-Processing
Software |
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Refinement | Method to determine structure: SIRAS / Resolution: 2.302→24.33 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.888 / SU B: 5.915 / SU ML: 0.148 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.268 / ESU R Free: 0.228
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 37.442 Å2
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Refinement step | Cycle: LAST / Resolution: 2.302→24.33 Å
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Refine LS restraints |
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Refine LS restraints NCS | Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION
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LS refinement shell | Resolution: 2.302→2.361 Å / Total num. of bins used: 20 /
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