+Open data
-Basic information
Entry | Database: PDB / ID: 3iw3 | ||||||
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Title | Crystal structure of hyperthermophilic nitrilase | ||||||
Components | Nitrilase | ||||||
Keywords | HYDROLASE / alpha-beta sandwich | ||||||
Function / homology | Function and homology information nitrilase / indole-3-acetonitrile nitrilase activity / N-carbamoylputrescine amidase activity / putrescine biosynthetic process from arginine / beta-alanine biosynthetic process via 3-ureidopropionate / beta-ureidopropionase activity Similarity search - Function | ||||||
Biological species | Pyrococcus abyssi (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||
Authors | Raczynska, J. / Vorgias, C. / Antranikian, G. / Rypniewski, W. | ||||||
Citation | Journal: J.Struct.Biol. / Year: 2010 Title: Crystallographic analysis of a thermoactive nitrilase. Authors: Raczynska, J.E. / Vorgias, C.E. / Antranikian, G. / Rypniewski, W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3iw3.cif.gz | 122.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3iw3.ent.gz | 94.7 KB | Display | PDB format |
PDBx/mmJSON format | 3iw3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3iw3_validation.pdf.gz | 448.7 KB | Display | wwPDB validaton report |
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Full document | 3iw3_full_validation.pdf.gz | 452.5 KB | Display | |
Data in XML | 3iw3_validation.xml.gz | 23.4 KB | Display | |
Data in CIF | 3iw3_validation.cif.gz | 33.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/iw/3iw3 ftp://data.pdbj.org/pub/pdb/validation_reports/iw/3iw3 | HTTPS FTP |
-Related structure data
Related structure data | 3ivzSC 3ki8C 3klcC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 29791.221 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pyrococcus abyssi (archaea) / Strain: GE5 / Gene: nit-30, PAB1449, PYRAB13990 / Plasmid: pET11a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9UYV8, beta-ureidopropionase #2: Chemical | #3: Chemical | ChemComp-MG / | #4: Water | ChemComp-HOH / | Sequence details | ACCORDING TO THE AUTHORS RESIDUE AT POSITION 238 IS MORE LIKELY A SER. | |
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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: 1.89 Å3/Da / Density % sol: 35.06 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 35% PEG 550MME, 0.2M MgCl2 or Mg(CH3COOH)2 and 0.2M TrisHCl pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X12 / Wavelength: 0.92918 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Dec 20, 2007 |
Radiation | Monochromator: Single crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.92918 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→20 Å / Num. all: 40685 / Num. obs: 40685 / % possible obs: 99.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.7 % / Rmerge(I) obs: 0.095 / Rsym value: 0.095 / Net I/σ(I): 16 |
Reflection shell | Resolution: 1.8→1.83 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.483 / Mean I/σ(I) obs: 3.2 / Rsym value: 0.483 / % possible all: 92.2 |
-Processing
Software | Name: REFMAC / Version: 5.5.0092 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3IVZ Resolution: 1.8→19.49 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.948 / SU B: 2.896 / SU ML: 0.089 / Cross valid method: THROUGHOUT / ESU R: 0.138 / ESU R Free: 0.13 / 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: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 19.849 Å2
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Refinement step | Cycle: LAST / Resolution: 1.8→19.49 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.799→1.846 Å / Total num. of bins used: 20
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