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Yorodumi- PDB-3onf: Crystal structure of Lupinus luteus S-adenosyl-L-homocysteine hyd... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3onf | ||||||
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Title | Crystal structure of Lupinus luteus S-adenosyl-L-homocysteine hydrolase in complex with cordycepin | ||||||
Components | Adenosylhomocysteinase | ||||||
Keywords | HYDROLASE/HYDROLASE INHIBITOR / Plant protein / enzyme-inhibitor complex / NAD cofactor / Regulation of SAM-dependent methylation reactions / HYDROLASE-HYDROLASE INHIBITOR complex | ||||||
Function / homology | Function and homology information adenosylhomocysteinase / adenosylhomocysteinase activity / S-adenosylmethionine cycle / one-carbon metabolic process / cytosol Similarity search - Function | ||||||
Biological species | Lupinus luteus (yellow lupine) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Brzezinski, K. / Jaskolski, M. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2012 Title: High-resolution structures of complexes of plant S-adenosyl-L-homocysteine hydrolase (Lupinus luteus). Authors: Brzezinski, K. / Dauter, Z. / Jaskolski, M. #1: Journal: Acta Crystallogr.,Sect.F / Year: 2008 Title: Purification, crystallization and preliminary crystallographic studies of plant S-adenosyl-L-homocysteine hydrolase (Lupinus luteus). Authors: Brzezinski, K. / Bujacz, G. / Jaskolski, M. #2: Journal: Acta Biochim.Pol. / Year: 2001 Title: Sequence determination and analysis of S-adenosyl-L-homocysteine hydrolase from yellow lupine (Lupinus luteus). Authors: Brzezinski, K. / Janowski, R. / Podkowinski, J. / Jaskolski, M. #3: Journal: Nat.Struct.Biol. / Year: 1998 Title: Structure determination of selenomethionyl S-adenosylhomocysteine hydrolase using data at a single wavelength. Authors: Turner, M.A. / Yuan, C.S. / Borchardt, R.T. / Hershfield, M.S. / Smith, G.D. / Howell, P.L. #4: Journal: Biochemistry / Year: 1999 Title: Crystal structure of S-adenosylhomocysteine hydrolase from rat liver. Authors: Hu, Y. / Komoto, J. / Huang, Y. / Gomi, T. / Ogawa, H. / Takata, Y. / Fujioka, M. / Takusagawa, F. #5: Journal: J.Mol.Biol. / Year: 2004 Title: Crystal structure of S-adenosyl-L-homocysteine hydrolase from the human malaria parasite Plasmodium falciparum. Authors: Tanaka, N. / Nakanishi, M. / Kusakabe, Y. / Shiraiwa, K. / Yabe, S. / Ito, Y. / Kitade, Y. / Nakamura, K.T. #6: Journal: Protein Sci. / Year: 2008 Title: Crystal structures of Mycobacterium tuberculosis S-adenosyl-L-homocysteine hydrolase in ternary complex with substrate and inhibitors. Authors: Reddy, M.C. / Kuppan, G. / Shetty, N.D. / Owen, J.L. / Ioerger, T.R. / Sacchettini, J.C. #7: Journal: MOL.PHYLOGENET.EVOL. / Year: 2005 Title: Bayesian phylogenetic analysis reveals two-domain topology of S-adenosylhomocysteine hydrolase protein sequences. Authors: Stepkowski, T. / Brzezinski, K. / Legocki, A.B. / Jaskolski, M. / Bena, G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3onf.cif.gz | 418.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3onf.ent.gz | 341.2 KB | Display | PDB format |
PDBx/mmJSON format | 3onf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3onf_validation.pdf.gz | 1.5 MB | Display | wwPDB validaton report |
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Full document | 3onf_full_validation.pdf.gz | 1.5 MB | Display | |
Data in XML | 3onf_validation.xml.gz | 43.6 KB | Display | |
Data in CIF | 3onf_validation.cif.gz | 64 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/on/3onf ftp://data.pdbj.org/pub/pdb/validation_reports/on/3onf | HTTPS FTP |
-Related structure data
Related structure data | 3ondC 3oneC 1v8bS 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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Details | The asymmetric unit contains a dimer, which corresponds to the biological unit |
-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 53673.336 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Lupinus luteus (yellow lupine) / Gene: SAHH, SHH, ssh-1 / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus (DE3)-RIPL / References: UniProt: Q9SP37, adenosylhomocysteinase |
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-Non-polymers , 5 types, 644 molecules
#2: Chemical | #3: Chemical | #4: Chemical | #5: Chemical | ChemComp-TRS / | #6: 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: 2.22 Å3/Da / Density % sol: 44.49 % |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 20% PEG 4000, 10% isopropanol, 0.1 M Tris-HCl pH 8.0, 2 mM cordycepin, VAPOR DIFFUSION, HANGING DROP, temperature 292K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X12 / Wavelength: 1 |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Feb 19, 2009 |
Radiation | Monochromator: DOUBLE CRYSTAL SI(111), HORIZONTALLY FOCUSING Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2→50 Å / Num. obs: 65547 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 10.5 % / Biso Wilson estimate: 22.7 Å2 / Rmerge(I) obs: 0.131 / Net I/σ(I): 17.5 |
Reflection shell | Resolution: 2→2.07 Å / Redundancy: 9.5 % / Rmerge(I) obs: 0.686 / Mean I/σ(I) obs: 3.1 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1V8B Resolution: 2→50 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.932 / SU B: 7.899 / SU ML: 0.098 Isotropic thermal model: Isotropic atomic displacement parameters Cross valid method: R FREE / ESU R: 0.165 / ESU R Free: 0.146 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGEN ATOMS WERE ADDED AT RIDING POSITIONS
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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: 18.72 Å2
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Refinement step | Cycle: LAST / Resolution: 2→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.05 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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