[English] 日本語
Yorodumi- PDB-3f0d: High resolution crystal structure of 2C-methyl-D-erythritol 2,4-c... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3f0d | ||||||
---|---|---|---|---|---|---|---|
Title | High resolution crystal structure of 2C-methyl-D-erythritol 2,4-cyclodiphosphatase synthase from Burkholderia pseudomallei | ||||||
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 / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.2 Å | ||||||
Authors | Seattle Structural Genomics Center for Infectious Disease (SSGCID) | ||||||
Citation | Journal: J Struct Funct Genomics / Year: 2011 Title: Leveraging structure determination with fragment screening for infectious disease drug targets: MECP synthase from Burkholderia pseudomallei. Authors: Begley, D.W. / Hartley, R.C. / Davies, D.R. / Edwards, T.E. / Leonard, J.T. / Abendroth, J. / Burris, C.A. / Bhandari, J. / Myler, P.J. / Staker, B.L. / Stewart, L.J. #1: 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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 3f0d.cif.gz | 360.6 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb3f0d.ent.gz | 294.5 KB | Display | PDB format |
PDBx/mmJSON format | 3f0d.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3f0d_validation.pdf.gz | 490.9 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 3f0d_full_validation.pdf.gz | 507 KB | Display | |
Data in XML | 3f0d_validation.xml.gz | 39.2 KB | Display | |
Data in CIF | 3f0d_validation.cif.gz | 55.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/f0/3f0d ftp://data.pdbj.org/pub/pdb/validation_reports/f0/3f0d | HTTPS FTP |
-Related structure data
Related structure data | 3f0eC 3f0gC 3ieqC 3iewC 3ikeC 3ikfC 3jvhC 3k14C 3k2xC 3mbmC 3p0zC 3p10C 3qhdC C: citing same article (ref.) |
---|---|
Similar structure data | |
Other databases |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 19487.109 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Details: Expressed as 3C protease cleavable, but not cleaved 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 #2: Chemical | ChemComp-ZN / #3: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.08 Å3/Da / Density % sol: 40.78 % |
---|---|
Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 8 Details: PACT screen condition c8, 0.1 M Tris HCL, 20% PEG 4000, 0.2 M NaCl, 34.4. mg/mL protein, 0.4 uL/0.4 uL drops, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 289K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 0.97934 Å |
Detector | Date: Aug 1, 2008 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97934 Å / Relative weight: 1 |
Reflection | Resolution: 1.2→50 Å / Num. obs: 271861 / % possible obs: 93.3 % / Redundancy: 4 % / Rmerge(I) obs: 0.081 / Net I/σ(I): 15.8 |
Reflection shell | Resolution: 1.2→1.29 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.52 / Mean I/σ(I) obs: 2.2 / Num. unique all: 24496 |
-Phasing
Phasing | Method: molecular replacement |
---|
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.2→50 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.943 / Occupancy max: 1 / Occupancy min: 0 / SU B: 1.222 / SU ML: 0.025 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.046 / ESU R Free: 0.045 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 53.62 Å2 / Biso mean: 20.638 Å2 / Biso min: 9.14 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.2→50 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.2→1.231 Å / Total num. of bins used: 20
|