+Open data
-Basic information
Entry | Database: PDB / ID: 4mv0 | ||||||
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Title | IspH in complex with pyridin-2-ylmethyl diphosphate | ||||||
Components | 4-hydroxy-3-methylbut-2-enyl diphosphate reductase | ||||||
Keywords | OXIDOREDUCTASE / Iron-sulfur cluster / Reductase / pyridin-2-ylmethyl diphosphate / Cytosol | ||||||
Function / homology | 4-hydroxy-3-methylbut-2-enyl diphosphate reductase, catalytic domain / Rossmann fold - #11270 / Cobalt-precorrin-4 Transmethylase; domain 1 / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta / pyridin-2-ylmethyl trihydrogen diphosphate / FE3-S4 CLUSTER / : Function and homology information | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | ||||||
Authors | Span, I. / Wang, K. / Song, Y. / Eisenreich, W. / Bacher, A. / Oldfield, E. / Groll, M. | ||||||
Citation | Journal: J.Am.Chem.Soc. / Year: 2014 Title: Insights into the Binding of Pyridines to the Iron-Sulfur Enzyme IspH. Authors: Span, I. / Wang, K. / Eisenreich, W. / Bacher, A. / Zhang, Y. / Oldfield, E. / Groll, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4mv0.cif.gz | 258.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4mv0.ent.gz | 209.9 KB | Display | PDB format |
PDBx/mmJSON format | 4mv0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4mv0_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 4mv0_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 4mv0_validation.xml.gz | 25.8 KB | Display | |
Data in CIF | 4mv0_validation.cif.gz | 36.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mv/4mv0 ftp://data.pdbj.org/pub/pdb/validation_reports/mv/4mv0 | HTTPS FTP |
-Related structure data
Related structure data | 4muxC 4muyC 4mv5C 3ke8S 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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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper:
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-Components
#1: Protein | Mass: 36107.941 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K-12 / Gene: ECDH1ME8569_0026, ispH / Plasmid: pQE30 / Production host: Escherichia coli (E. coli) / Strain (production host): XL-1 blue References: UniProt: C9QSC3, 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: 2.17 Å3/Da / Density % sol: 43.23 % |
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Crystal grow | Temperature: 293 K / pH: 6.5 Details: 0.1 M BIS-TRIS, 0.2 M ammonium sulfate, 25% PEG3350, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å |
Detector | Type: PSI PILATUS 6M / Detector: PIXEL / Date: Dec 5, 2012 |
Radiation | Monochromator: double-crystal fixed-exit monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→30 Å / Num. all: 50202 / Num. obs: 49549 / % possible obs: 98.7 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 6.9 % / Rsym value: 0.09 / Net I/σ(I): 11.37 |
Reflection shell | Resolution: 1.9→2 Å / Mean I/σ(I) obs: 2.82 / Rsym value: 0.421 / % possible all: 95.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3KE8 Resolution: 1.9→14.97 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.934 / SU B: 9.504 / SU ML: 0.141 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE
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Solvent computation | Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 36.53 Å2
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Refinement step | Cycle: LAST / Resolution: 1.9→14.97 Å
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Refine LS restraints |
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