+Open data
-Basic information
Entry | Database: PDB / ID: 2ive | ||||||
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Title | Structure of protoporphyrinogen oxidase from Myxococcus xanthus | ||||||
Components | PROTOPORPHYRINOGEN OXIDASE | ||||||
Keywords | OXIDOREDUCTASE / PROTOPORPHYRINOGEN OXIDASE / PORPHYRIN BIOSYNTHESIS / CHLOROPHYLL BIOSYNTHESIS / FAD / PORPHYRIA / FLAVOPROTEIN / HEME BIOSYNTHESIS / HAEM BIOSYNTHESIS | ||||||
Function / homology | Function and homology information protoporphyrinogen oxidase / oxygen-dependent protoporphyrinogen oxidase activity / protoporphyrinogen IX biosynthetic process / plasma membrane / cytoplasm Similarity search - Function | ||||||
Biological species | MYXOCOCCUS XANTHUS (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å | ||||||
Authors | Corradi, H.R. / Corrigall, A.V. / Boix, E. / Mohan, C.G. / Sturrock, E.D. / Meissner, P.N. / Acharya, K.R. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2006 Title: Crystal Structure of Protoporphyrinogen Oxidase from Myxococcus Xanthus and its Complex with the Inhibitor Acifluorfen. Authors: Corradi, H.R. / Corrigall, A.V. / Boix, E. / Mohan, C.G. / Sturrock, E.D. / Meissner, P.N. / Acharya, K.R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2ive.cif.gz | 185.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2ive.ent.gz | 145.7 KB | Display | PDB format |
PDBx/mmJSON format | 2ive.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2ive_validation.pdf.gz | 1.5 MB | Display | wwPDB validaton report |
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Full document | 2ive_full_validation.pdf.gz | 1.5 MB | Display | |
Data in XML | 2ive_validation.xml.gz | 23.7 KB | Display | |
Data in CIF | 2ive_validation.cif.gz | 33.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/iv/2ive ftp://data.pdbj.org/pub/pdb/validation_reports/iv/2ive | HTTPS FTP |
-Related structure data
Related structure data | 2ivdC 1sezS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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Components on special symmetry positions |
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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (-0.68436, 0.72908, 0.01024), Vector: |
-Components
#1: Protein | Mass: 50396.566 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) MYXOCOCCUS XANTHUS (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): JM109 / References: UniProt: P56601 #2: Chemical | #3: Chemical | ChemComp-GOL / #4: Chemical | #5: Water | ChemComp-HOH / | Compound details | PROTOPORPH | Sequence details | THE FIRST MET IN THE PPOX SEQUENCE WAS REPLACED BY THE HIS TAG IN THE CONSTRUCT, BUT THIS RESIDUE ...THE FIRST MET IN THE PPOX SEQUENCE WAS REPLACED BY THE HIS TAG IN THE CONSTRUCT, BUT THIS RESIDUE WAS NOT OBSERVED IN THE STRUCTURE | |
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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: 3.74 Å3/Da / Density % sol: 66.85 % |
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Crystal grow | pH: 7.5 Details: 0.1M TRIS/HCL PH 7.5, 1.5M AMMONIUM SULPHATE, 20% GLYCEROL, 1% PEG 4000 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SRS / Beamline: PX14.2 / Wavelength: 0.978 |
Detector | Type: ADSC CCD / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.978 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→74.3 Å / Num. obs: 41382 / % possible obs: 100 % / Observed criterion σ(I): 2 / Redundancy: 7.5 % / Rmerge(I) obs: 0.14 / Net I/σ(I): 14.7 |
Reflection shell | Resolution: 2.7→2.85 Å / Rmerge(I) obs: 0.57 / Mean I/σ(I) obs: 2.6 / % possible all: 99.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1SEZ Resolution: 2.7→74.33 Å / Cor.coef. Fo:Fc: 0.889 / Cor.coef. Fo:Fc free: 0.849 / SU B: 12.894 / SU ML: 0.262 / Cross valid method: THROUGHOUT / ESU R: 0.496 / ESU R Free: 0.323 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. RESIDUES 87-93 IN BOTH MOLECULES COULD NOT BE MODELLED VERY ACCURATELY DUE TO LOTS OF NOISE IN THE MAPS
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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: 30.6 Å2
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Refinement step | Cycle: LAST / Resolution: 2.7→74.33 Å
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