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Yorodumi- PDB-4dhd: Crystal structure of isoprenoid synthase A3MSH1 (TARGET EFI-50199... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4dhd | ||||||
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Title | Crystal structure of isoprenoid synthase A3MSH1 (TARGET EFI-501992) from Pyrobaculum calidifontis | ||||||
Components | Polyprenyl synthetase | ||||||
Keywords | TRANSFERASE / ISOPRENOID SYNTHESIS / ISOPRENOID DIPHOSPHATE SYNTHASE / Structural Genomics | ||||||
Function / homology | Function and homology information plastoquinone biosynthetic process / geranylgeranyl diphosphate biosynthetic process / transferase complex / farnesyltranstransferase activity / ubiquinone biosynthetic process / metal ion binding Similarity search - Function | ||||||
Biological species | Pyrobaculum calidifontis (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å | ||||||
Authors | Patskovsky, Y. / Toro, R. / Bhosle, R. / Hillerich, B. / Seidel, R.D. / Washington, E. / Scott Glenn, A. / Chowdhury, S. / Evans, B. / Hammonds, J. ...Patskovsky, Y. / Toro, R. / Bhosle, R. / Hillerich, B. / Seidel, R.D. / Washington, E. / Scott Glenn, A. / Chowdhury, S. / Evans, B. / Hammonds, J. / Zencheck, W.D. / Imker, H.J. / Poulter, C.D. / Gerlt, J.A. / Almo, S.C. / Enzyme Function Initiative (EFI) | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2013 Title: Prediction of function for the polyprenyl transferase subgroup in the isoprenoid synthase superfamily. Authors: Wallrapp, F.H. / Pan, J.J. / Ramamoorthy, G. / Almonacid, D.E. / Hillerich, B.S. / Seidel, R. / Patskovsky, Y. / Babbitt, P.C. / Almo, S.C. / Jacobson, M.P. / Poulter, C.D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4dhd.cif.gz | 85.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4dhd.ent.gz | 62.6 KB | Display | PDB format |
PDBx/mmJSON format | 4dhd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4dhd_validation.pdf.gz | 444.5 KB | Display | wwPDB validaton report |
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Full document | 4dhd_full_validation.pdf.gz | 445.9 KB | Display | |
Data in XML | 4dhd_validation.xml.gz | 16.5 KB | Display | |
Data in CIF | 4dhd_validation.cif.gz | 24.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dh/4dhd ftp://data.pdbj.org/pub/pdb/validation_reports/dh/4dhd | HTTPS FTP |
-Related structure data
Related structure data | 3lomC 3lvsC 3mzvC 3nf2C 3oyrC 3p41C 3p8lC 3p8rC 3pdeC 3pkoC 3q1oC 3q2qC 3qqvC 3rmgC 3ts7C 3ucaC 4f62C 4fp4C 1wy0S 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
#1: Protein | Mass: 40151.848 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pyrobaculum calidifontis (archaea) / Strain: JCM 11548/VA1 / Gene: Pcal_0150 / Plasmid: PET / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A3MSH1 |
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#2: Chemical | ChemComp-PO4 / |
#3: Chemical | ChemComp-CL / |
#4: Chemical | ChemComp-ACT / |
#5: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.56 Å3/Da / Density % sol: 52.06 % |
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Crystal grow | pH: 5.5 Details: 0.1M BIS-TRIS, 25% PEG3350, PH 5.5, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 294 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.075 |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 11, 2011 / Details: MIRRORS |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.075 Å / Relative weight: 1 |
Reflection | Resolution: 1.65→70 Å / Num. obs: 49409 / % possible obs: 93.8 % / Observed criterion σ(I): -5 / Redundancy: 7.7 % / Biso Wilson estimate: 22.442 Å2 / Rsym value: 0.117 / Net I/σ(I): 9.9 |
Reflection shell | Resolution: 1.65→1.68 Å / Redundancy: 8 % / Rmerge(I) obs: 0.36 / Mean I/σ(I) obs: 3.8 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1WY0 Resolution: 1.65→50 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.946 / SU B: 1.597 / SU ML: 0.055 / Cross valid method: THROUGHOUT / ESU R: 0.092 / ESU R Free: 0.093 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 27.387 Å2
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Refinement step | Cycle: LAST / Resolution: 1.65→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.65→1.697 Å / Total num. of bins used: 20
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