+Open data
-Basic information
Entry | Database: PDB / ID: 2v7j | ||||||
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Title | PrnB L-tryptophan complex | ||||||
Components | PRNB | ||||||
Keywords | BIOSYNTHETIC PROTEIN / HEME / IDO / TDO | ||||||
Function / homology | Function and homology information Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen; With oxidation of a pair of donors resulting in the reduction of O2 to two molecules of water / tryptophan catabolic process to kynurenine / antibiotic biosynthetic process / oxidoreductase activity / heme binding / metal ion binding Similarity search - Function | ||||||
Biological species | PSEUDOMONAS FLUORESCENS (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2 Å | ||||||
Authors | Naismith, J.H. | ||||||
Citation | Journal: Biochemistry / Year: 2007 Title: The Second Enzyme in Pyrrolnitrin Biosynthetic Pathway is Related to the Heme-Dependent Dioxygenase Superfamily Authors: De Laurentis, W. / Khim, L. / Anderson, J.L.R. / Adam, A. / Phillips, R.S. / Chapman, S.K. / Van Pee, K.-H. / Naismith, J.H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2v7j.cif.gz | 78.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2v7j.ent.gz | 63.1 KB | Display | PDB format |
PDBx/mmJSON format | 2v7j.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/v7/2v7j ftp://data.pdbj.org/pub/pdb/validation_reports/v7/2v7j | HTTPS FTP |
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-Related 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: 39917.492 Da / Num. of mol.: 1 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) PSEUDOMONAS FLUORESCENS (bacteria) / Production host: PSEUDOMONAS FLUORESCENS (bacteria) / References: UniProt: P95481 | ||||||
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#2: Chemical | ChemComp-TRP / | ||||||
#3: Chemical | ChemComp-HEM / | ||||||
#4: Chemical | #5: Water | ChemComp-HOH / | Compound details | ENGINEERED RESIDUE IN CHAIN A, CYS 21 TO SER ENGINEERED RESIDUE IN CHAIN A, CYS 60 TO SER ...ENGINEERED | Sequence details | TRIPLE MUTANT CRYSTALLIZ | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.06 Å3/Da / Density % sol: 60 % / Description: NONE |
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Crystal grow | pH: 7.5 / Details: pH 7.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 1.739 |
Detector | Type: ADSC CCD / Detector: CCD |
Radiation | Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.739 Å / Relative weight: 1 |
Reflection | Resolution: 2→51 Å / Num. obs: 30217 / % possible obs: 97 % / Observed criterion σ(I): 0 / Redundancy: 7 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 21 |
Reflection shell | Resolution: 2→2.11 Å / Redundancy: 7 % / Rmerge(I) obs: 0.3 / Mean I/σ(I) obs: 6 / % possible all: 94 |
-Processing
Software |
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Refinement | Method to determine structure: MAD Starting model: NONE Resolution: 2→51.1 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.943 / SU B: 5.926 / SU ML: 0.085 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.143 / ESU R Free: 0.131 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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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: 29.89 Å2
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Refinement step | Cycle: LAST / Resolution: 2→51.1 Å
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Refine LS restraints |
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