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Yorodumi- PDB-2x67: The ternary complex of PrnB (the second enzyme in pyrrolnitrin bi... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2x67 | ||||||
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Title | The ternary complex of PrnB (the second enzyme in pyrrolnitrin biosynthesis pathway), tryptophan and cyanide | ||||||
Components | PRNB | ||||||
Keywords | BIOSYNTHETIC PROTEIN / INDOLAMINE/TRYPTOPHAN DIOXYGENASE SUPERFAMILY | ||||||
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 / MOLECULAR REPLACEMENT / Resolution: 2.16 Å | ||||||
Authors | Zhu, X. / van pee, K.-H. / Naismith, J.H. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2010 Title: The Ternary Complex of Prnb (the Second Enzyme in Pyrrolnitrin Biosynthesis Pathway), Tryptophan and Cyanide Yields New Mechanistic Insights Into the Indolamine Dioxygenase Superfamily. Authors: Zhu, X. / 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 | 2x67.cif.gz | 92 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2x67.ent.gz | 68.7 KB | Display | PDB format |
PDBx/mmJSON format | 2x67.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/x6/2x67 ftp://data.pdbj.org/pub/pdb/validation_reports/x6/2x67 | HTTPS FTP |
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-Related structure data
Related structure data | 2x66C 2x68C 2v7jS 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
-Protein , 1 types, 1 molecules A
#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) / Strain: BL915 / Plasmid: PCIBHISTEVPRNB_TRIPLE_CYSMUTANT / Production host: PSEUDOMONAS FLUORESCENS (bacteria) / Strain (production host): BL915 / Variant (production host): DELTAORF(PRNA-PRND) / References: UniProt: P95481 |
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-Non-polymers , 5 types, 309 molecules
#2: Chemical | ChemComp-HEM / | ||||
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#3: Chemical | ChemComp-TRP / | ||||
#4: Chemical | #5: Chemical | ChemComp-CYN / | #6: Water | ChemComp-HOH / | |
-Details
Compound details | ENGINEERED RESIDUE IN CHAIN A, CYS 21 TO SER ENGINEERED RESIDUE IN CHAIN A, CYS 60 TO SER ...ENGINEERED |
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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: 2.9 Å3/Da / Density % sol: 57.97 % / Description: NONE |
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Crystal grow | pH: 6.4 Details: 0.1M BIS-TRIS BUFFER PH 6.4, 10% PEG3350, 0.2M MGSO4 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 |
Detector | Type: RIGAKU CCD / Detector: CCD / Date: Apr 17, 2008 / Details: OSMIC MIRRORS |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.16→30 Å / Num. obs: 24411 / % possible obs: 99.8 % / Observed criterion σ(I): 2 / Redundancy: 3.5 % / Biso Wilson estimate: 27.2 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 15.6 |
Reflection shell | Resolution: 2.16→2.2 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.46 / Mean I/σ(I) obs: 3.4 / % possible all: 99.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2V7J Resolution: 2.16→29.84 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.934 / SU B: 9.596 / SU ML: 0.112 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.188 / ESU R Free: 0.166 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY.
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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: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 15.024 Å2
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Refinement step | Cycle: LAST / Resolution: 2.16→29.84 Å
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Refine LS restraints |
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