+Open data
-Basic information
Entry | Database: PDB / ID: 1zz7 | ||||||
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Title | Crystal Structure of FeII HppE in Complex with Substrate form 1 | ||||||
Components | Hydroxyprophylphosphonic Acid Epoxidase | ||||||
Keywords | OXIDOREDUCTASE / Substrate-Enzyme Complex / Cupin / Mononuclear Iron Enzyme | ||||||
Function / homology | Function and homology information (S)-2-hydroxypropylphosphonic acid epoxidase / phosphinothricin biosynthetic process / oxidoreductase activity, acting on paired donors, with oxidation of a pair of donors resulting in the reduction of molecular oxygen to two molecules of water / dioxygenase activity / antibiotic biosynthetic process / ferrous iron binding / protein homotetramerization / DNA binding Similarity search - Function | ||||||
Biological species | Streptomyces wedmorensis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / RIGID BODY REFINEMENT / Resolution: 2.1 Å | ||||||
Authors | Higgins, L.J. / Yan, F. / Liu, P. / Liu, H.W. / Drennan, C.L. | ||||||
Citation | Journal: Nature / Year: 2005 Title: Structural insight into antibiotic fosfomycin biosynthesis by a mononuclear iron enzyme Authors: Higgins, L.J. / Yan, F. / Liu, P. / Liu, H.W. / Drennan, C.L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1zz7.cif.gz | 81.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1zz7.ent.gz | 60.5 KB | Display | PDB format |
PDBx/mmJSON format | 1zz7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1zz7_validation.pdf.gz | 456.2 KB | Display | wwPDB validaton report |
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Full document | 1zz7_full_validation.pdf.gz | 461.5 KB | Display | |
Data in XML | 1zz7_validation.xml.gz | 17.3 KB | Display | |
Data in CIF | 1zz7_validation.cif.gz | 23.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zz/1zz7 ftp://data.pdbj.org/pub/pdb/validation_reports/zz/1zz7 | HTTPS FTP |
-Related structure data
Related structure data | 1zz6C 1zz8C 1zz9C 1zzbC 1zzcSC 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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Unit cell |
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-Components
#1: Protein | Mass: 21361.127 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptomyces wedmorensis (bacteria) / Gene: fom4 / Plasmid: pET24b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) References: UniProt: Q56185, Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen #2: Chemical | #3: Chemical | #4: 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: 2.8 Å3/Da / Density % sol: 55.5 % |
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Crystal grow | pH: 8.5 / Details: 2.0M Ammonium Sulfate, 0.1M Tris-HCL, pH 8.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 8-BM / Wavelength: 0.9791 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9791 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→30 Å / Num. obs: 28639 / % possible obs: 97.4 % / Redundancy: 6.9 % / Biso Wilson estimate: 28.9 Å2 / Rsym value: 0.083 / Net I/σ(I): 19.1 |
Reflection shell | Resolution: 2.1→2.18 Å / Mean I/σ(I) obs: 3.2 / Rsym value: 0.362 / % possible all: 93.1 |
-Processing
Software |
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Refinement | Method to determine structure: RIGID BODY REFINEMENT Starting model: PDB entry 1ZZC Resolution: 2.1→29.03 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 445830.97 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: MLFL
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 46.12 Å2 / ksol: 0.37 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 34.7 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.1→29.03 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.1→2.23 Å / Total num. of bins used: 6
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Xplor file |
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