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Yorodumi- PDB-3f0f: Co-crystal structure of 2C-methyl-D-erythritol 2,4-cyclodiphospha... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3f0f | ||||||
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Title | Co-crystal structure of 2C-methyl-D-erythritol 2,4-cyclodiphosphate synthase from Burkholderia pseudomallei with hydrolyzed CDP | ||||||
Components | 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase | ||||||
Keywords | LYASE / SSGCID / NIAID / Burkholderia pseudomallei / Isoprene biosynthesis / Metal-binding / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease | ||||||
Function / homology | Function and homology information 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase / 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase activity / isopentenyl diphosphate biosynthetic process, methylerythritol 4-phosphate pathway / terpenoid biosynthetic process / metal ion binding Similarity search - Function | ||||||
Biological species | Burkholderia pseudomallei (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.09 Å | ||||||
Authors | Seattle Structural Genomics Center for Infectious Disease (SSGCID) | ||||||
Citation | Journal: Plos One / Year: 2013 Title: Combining functional and structural genomics to sample the essential Burkholderia structome. Authors: Baugh, L. / Gallagher, L.A. / Patrapuvich, R. / Clifton, M.C. / Gardberg, A.S. / Edwards, T.E. / Armour, B. / Begley, D.W. / Dieterich, S.H. / Dranow, D.M. / Abendroth, J. / Fairman, J.W. / ...Authors: Baugh, L. / Gallagher, L.A. / Patrapuvich, R. / Clifton, M.C. / Gardberg, A.S. / Edwards, T.E. / Armour, B. / Begley, D.W. / Dieterich, S.H. / Dranow, D.M. / Abendroth, J. / Fairman, J.W. / Fox, D. / Staker, B.L. / Phan, I. / Gillespie, A. / Choi, R. / Nakazawa-Hewitt, S. / Nguyen, M.T. / Napuli, A. / Barrett, L. / Buchko, G.W. / Stacy, R. / Myler, P.J. / Stewart, L.J. / Manoil, C. / Van Voorhis, W.C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3f0f.cif.gz | 108.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3f0f.ent.gz | 80.3 KB | Display | PDB format |
PDBx/mmJSON format | 3f0f.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/f0/3f0f ftp://data.pdbj.org/pub/pdb/validation_reports/f0/3f0f | HTTPS FTP |
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-Related structure data
Related structure data | 3d63C 3dahC 3eizC 3ej2C 3ek2C 3ezoC 3ftpC 3gk0C 3gk3C 3gvfC 3gwaC 3gweC 3imlC 3sz8C 3t4cC 3tmlC 3tmqC 3txyC 3u7jC 3ue9C 3uk1C 3uk2C 3undC 3uptC 3urrC 3uw1C 3uw2C 3uw3C 3v2iC 3v7nC 3v8hC 3v9oC 3v9pC 3vavC 4ddoC 4dfeC 4dheC 4dhkC 4dutC 4dz4C 4e4tC 4efiC 4eg0C 4egjC 4ek2C 4eqyC 4ewgC 4exqC 4f2gC 4f32C 4f3nC 4f3yC 4f4hC 4f7dC 4fk8C 4fryC 4g1kC 4g67C 4ghkC 4h3yC 4h3zC 4h4gC 3f0dS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | |
Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein , 1 types, 3 molecules ABC
#1: Protein | Mass: 19487.109 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Details: Expressed with an N-terminal hexahis tag and 3C protease cleavage site, although construct was not cleaved prior to crystallization Source: (gene. exp.) Burkholderia pseudomallei (bacteria) / Strain: 1710b / Gene: ispF, mecS, BPSL2098 / Plasmid: AVA0421 / Production host: Escherichia coli (E. coli) References: UniProt: Q63T71, UniProt: Q3JRA0*PLUS, 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase |
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-Non-polymers , 5 types, 209 molecules
#2: Chemical | ChemComp-GOL / | ||||
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#3: Chemical | ChemComp-MG / | ||||
#4: Chemical | #5: Chemical | ChemComp-C5P / | #6: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.98 Å3/Da / Density % sol: 37.97 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop Details: 34.4 mg/mL protein, Crystal ID 200564d9, VAPOR DIFFUSION, SITTING DROP, temperature 289K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54178 Å |
Detector | Type: RIGAKU SATURN 944 / Detector: CCD / Date: Sep 19, 2008 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54178 Å / Relative weight: 1 |
Reflection | Resolution: 2.09→65.8 Å / Num. obs: 27899 / % possible obs: 98.8 % / Redundancy: 5.1 % / Rmerge(I) obs: 0.098 / Χ2: 1.145 / Net I/σ(I): 15.889 |
Reflection shell | Resolution: 2.09→2.18 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.549 / Mean I/σ(I) obs: 2.5 / Num. unique all: 2729 / Χ2: 0.95 / % possible all: 98.4 |
-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: pdb entry 3F0D Resolution: 2.09→50 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.923 / WRfactor Rfree: 0.241 / WRfactor Rwork: 0.19 / Occupancy max: 1 / Occupancy min: 1 / SU B: 5.24 / SU ML: 0.14 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.242 / ESU R Free: 0.199 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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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 max: 63.33 Å2 / Biso mean: 31.043 Å2 / Biso min: 14.95 Å2
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Refinement step | Cycle: LAST / Resolution: 2.09→50 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20
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