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Yorodumi- PDB-3mgk: CRYSTAL STRUCTURE OF PROBABLE PROTEASE/AMIDASE FROM Clostridium a... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3mgk | ||||||
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Title | CRYSTAL STRUCTURE OF PROBABLE PROTEASE/AMIDASE FROM Clostridium acetobutylicum ATCC 824 | ||||||
Components | Intracellular protease/amidase related enzyme (ThiJ family) | ||||||
Keywords | structural genomics / unknown function / AMIDOTRANFERASE-LIKE / PSI / PROTEIN STRUCTURE INITIATIVE / NYSGRC / NEW YORK STRUCTURAL GENOMIX RESEARCH CONSORTIUM / NYSGXRC / New York SGX Research Center for Structural Genomics | ||||||
Function / homology | DJ-1/PfpI / DJ-1/PfpI family / Class I glutamine amidotransferase (GATase) domain / Class I glutamine amidotransferase-like / peptidase activity / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta / Intracellular protease/amidase related enzyme (ThiJ family) Function and homology information | ||||||
Biological species | Clostridium acetobutylicum (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2 Å | ||||||
Authors | Patskovsky, Y. / Toro, R. / Freeman, J. / Iizuka, M. / Sauder, J.M. / Burley, S.K. / Almo, S.C. / New York SGX Research Center for Structural Genomics (NYSGXRC) | ||||||
Citation | Journal: To be Published Title: CRYSTAL STRUCTURE OF PROBABLE PROTEASE/AMIDASE FROM Clostridium acetobutylicum Authors: Patskovsky, Y. / Toro, R. / Freeman, J. / Iizuka, M. / Sauder, J.M. / Burley, S.K. / 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 | 3mgk.cif.gz | 94.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3mgk.ent.gz | 73.1 KB | Display | PDB format |
PDBx/mmJSON format | 3mgk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mg/3mgk ftp://data.pdbj.org/pub/pdb/validation_reports/mg/3mgk | 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: 23974.822 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Clostridium acetobutylicum (bacteria) / Gene: CA_C2826 / Production host: Escherichia coli (E. coli) / References: UniProt: Q97FB4 #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: 2.21 Å3/Da / Density % sol: 44.29 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 0.1M BIS-TRIS, PH 6.5, 25% PEG3350, 200MM AMMONIUM ACETATE, 10% GLYCEROL, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 294K |
-Data collection
Diffraction | Mean temperature: 93 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.979 |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 28, 2010 / 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: 2→40 Å / Num. obs: 28333 / % possible obs: 99.5 % / Observed criterion σ(I): -5 / Redundancy: 3.2 % / Rsym value: 0.062 / Net I/σ(I): 9 |
Reflection shell | Resolution: 2→2.07 Å / Redundancy: 3 % / Mean I/σ(I) obs: 1.3 / Rsym value: 0.77 / % possible all: 95.8 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2→20 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.952 / SU B: 6.767 / SU ML: 0.176 / Cross valid method: THROUGHOUT / ESU R: 0.189 / ESU R Free: 0.174 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 55.627 Å2
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Refinement step | Cycle: LAST / Resolution: 2→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.051 Å / Total num. of bins used: 20
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