+Open data
-Basic information
Entry | Database: PDB / ID: 3kem | ||||||
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Title | Crystal structure of IspH:IPP complex | ||||||
Components | 4-hydroxy-3-methylbut-2-enyl diphosphate reductase | ||||||
Keywords | OXIDOREDUCTASE / IspH / lytB / iron sulfure protein / malaria / tuberculosis / non-mevalonic acid pathway / Iron / Iron-sulfur / Isoprene biosynthesis / Metal-binding / NADP | ||||||
Function / homology | Function and homology information hydroxymethylbutenyl pyrophosphate reductase activity / 4-hydroxy-3-methylbut-2-en-1-yl diphosphate reductase / 4-hydroxy-3-methylbut-2-enyl diphosphate reductase activity / dimethylallyl diphosphate biosynthetic process / isopentenyl diphosphate biosynthetic process, methylerythritol 4-phosphate pathway / terpenoid biosynthetic process / 3 iron, 4 sulfur cluster binding / 4 iron, 4 sulfur cluster binding / metal ion binding / cytosol Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Groll, M. / Graewert, T. / Span, I. / Eisenreich, W. / Bacher, A. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2010 Title: Probing the reaction mechanism of IspH protein by x-ray structure analysis. Authors: Grawert, T. / Span, I. / Eisenreich, W. / Rohdich, F. / Eppinger, J. / Bacher, A. / Groll, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3kem.cif.gz | 142.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3kem.ent.gz | 110.9 KB | Display | PDB format |
PDBx/mmJSON format | 3kem.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3kem_validation.pdf.gz | 476.8 KB | Display | wwPDB validaton report |
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Full document | 3kem_full_validation.pdf.gz | 494.3 KB | Display | |
Data in XML | 3kem_validation.xml.gz | 31 KB | Display | |
Data in CIF | 3kem_validation.cif.gz | 44.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ke/3kem ftp://data.pdbj.org/pub/pdb/validation_reports/ke/3kem | HTTPS FTP |
-Related structure data
Related structure data | 3ke8C 3ke9C 3kefC 3kelC 3dnfS 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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2 |
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3 |
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Unit cell |
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-Components
#1: Protein | Mass: 36078.902 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K-12 / Gene: b0029, ispH, JW0027, lytB, yaaE / Plasmid: pQE30 / Production host: Escherichia coli (E. coli) / Strain (production host): XL1 References: UniProt: P62623, 4-hydroxy-3-methylbut-2-enyl diphosphate reductase #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: 2.28 Å3/Da / Density % sol: 45.98 % |
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Crystal grow | Method: vapor diffusion, sitting drop / pH: 6.5 Details: 0.1M Bis-Tris, 0.2M Li2SO4, 25% PEG 3350, pH 6.5, VAPOR DIFFUSION, SITTING DROP |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: Cu FINE FOCUS / Wavelength: 1.5418 Å |
Detector | Type: Bruker Platinum 135 / Detector: CCD / Date: Sep 5, 2009 |
Radiation | Monochromator: Ni-Filter / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2→65 Å / Num. obs: 39891 / % possible obs: 100 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 3 / Redundancy: 12 % / Biso Wilson estimate: 7.8 Å2 / Rmerge(I) obs: 0.048 / Net I/σ(I): 17.6 |
Reflection shell | Resolution: 2→2.1 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.243 / Mean I/σ(I) obs: 4 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3DNF Resolution: 2→9.99 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 3127385.21 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 2 / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 71.9695 Å2 / ksol: 0.5 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 20.1 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2→9.99 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.12 Å / Rfactor Rfree error: 0.019 / Total num. of bins used: 6
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Xplor file |
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