+Open data
-Basic information
Entry | Database: PDB / ID: 1sez | ||||||
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Title | Crystal Structure of Protoporphyrinogen IX Oxidase | ||||||
Components | Protoporphyrinogen oxidase, mitochondrial | ||||||
Keywords | OXIDOREDUCTASE / FAD-binding / Para-hydroxy-benzoate-hydroxylase fold (PHBH-fold) / monotopic membrane-binding domain | ||||||
Function / homology | Function and homology information protoporphyrinogen oxidase / oxygen-dependent protoporphyrinogen oxidase activity / protoporphyrinogen IX biosynthetic process / chloroplast / oxidoreductase activity / mitochondrion Similarity search - Function | ||||||
Biological species | Nicotiana tabacum (common tobacco) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.9 Å | ||||||
Authors | Koch, M. / Breithaupt, C. / Kiefersauer, R. / Freigang, J. / Huber, R. / Messerschmidt, A. | ||||||
Citation | Journal: Embo J. / Year: 2004 Title: Crystal structure of protoporphyrinogen IX oxidase: a key enzyme in haem and chlorophyll biosynthesis. Authors: Koch, M. / Breithaupt, C. / Kiefersauer, R. / Freigang, J. / Huber, R. / Messerschmidt, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1sez.cif.gz | 192 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1sez.ent.gz | 159.5 KB | Display | PDB format |
PDBx/mmJSON format | 1sez.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1sez_validation.pdf.gz | 1.8 MB | Display | wwPDB validaton report |
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Full document | 1sez_full_validation.pdf.gz | 1.9 MB | Display | |
Data in XML | 1sez_validation.xml.gz | 42 KB | Display | |
Data in CIF | 1sez_validation.cif.gz | 56.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/se/1sez ftp://data.pdbj.org/pub/pdb/validation_reports/se/1sez | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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Details | The second subunit of the biological assembly is generated by the two fold axis: x, -y, -z+1 |
-Components
#1: Protein | Mass: 55902.094 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Nicotiana tabacum (common tobacco) / Gene: PPXII, PPOX2 / Plasmid: pET32a-PPO2NT / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: O24164, protoporphyrinogen oxidase #2: Chemical | #3: Chemical | #4: Chemical | #5: 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: 2.78 Å3/Da / Density % sol: 55.43 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4 Details: PEG 1000, sodium citrate, sodium chloride, pH 4.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.979 |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 23, 2003 / Details: Si-monochromator |
Radiation | Monochromator: Si-mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 2.9→19.73 Å / Num. all: 25016 / Num. obs: 24891 / % possible obs: 99.5 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 3.8 % / Biso Wilson estimate: 83 Å2 / Rmerge(I) obs: 0.079 / Rsym value: 0.079 / Net I/σ(I): 11.6 |
Reflection shell | Resolution: 2.9→3 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.528 / Mean I/σ(I) obs: 2.8 / Num. unique all: 2083 / Rsym value: 0.528 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.9→19.73 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 2.5 / σ(I): 2.5 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 66.3 Å2
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Refine analyze | Luzzati coordinate error obs: 0.418 Å / Luzzati d res low obs: 10 Å | |||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.9→19.73 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.9→2.94 Å
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