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Yorodumi- PDB-1a7a: STRUCTURE OF HUMAN PLACENTAL S-ADENOSYLHOMOCYSTEINE HYDROLASE: DE... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1a7a | ||||||
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Title | STRUCTURE OF HUMAN PLACENTAL S-ADENOSYLHOMOCYSTEINE HYDROLASE: DETERMINATION OF A 30 SELENIUM ATOM SUBSTRUCTURE FROM DATA AT A SINGLE WAVELENGTH | ||||||
Components | S-ADENOSYLHOMOCYSTEINE HYDROLASE | ||||||
Keywords | HYDROLASE / NAD BINDING PROTEIN | ||||||
Function / homology | Function and homology information Defective AHCY causes HMAHCHD / Sulfur amino acid metabolism / Metabolism of ingested SeMet, Sec, MeSec into H2Se / adenosylhomocysteinase / adenosylhomocysteinase activity / S-adenosylmethionine cycle / Methylation / melanosome / one-carbon metabolic process / endoplasmic reticulum ...Defective AHCY causes HMAHCHD / Sulfur amino acid metabolism / Metabolism of ingested SeMet, Sec, MeSec into H2Se / adenosylhomocysteinase / adenosylhomocysteinase activity / S-adenosylmethionine cycle / Methylation / melanosome / one-carbon metabolic process / endoplasmic reticulum / extracellular exosome / nucleus / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAS / Resolution: 2.8 Å | ||||||
Authors | Turner, M.A. / Yuan, C.-S. / Borchardt, R.T. / Hershfield, M.S. / Smith, G.D. / Howell, P.L. | ||||||
Citation | 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. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1a7a.cif.gz | 173.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1a7a.ent.gz | 146 KB | Display | PDB format |
PDBx/mmJSON format | 1a7a.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1a7a_validation.pdf.gz | 952.7 KB | Display | wwPDB validaton report |
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Full document | 1a7a_full_validation.pdf.gz | 1000.4 KB | Display | |
Data in XML | 1a7a_validation.xml.gz | 38.6 KB | Display | |
Data in CIF | 1a7a_validation.cif.gz | 51.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/a7/1a7a ftp://data.pdbj.org/pub/pdb/validation_reports/a7/1a7a | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (-0.972, -0.234, -0.005), Vector: |
-Components
#1: Protein | Mass: 48522.281 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: SELENOMETHIONINE DERIVATIZED PROTEIN / Source: (gene. exp.) Homo sapiens (human) / Tissue: PLACENTA / Cellular location (production host): CYTOPLASM / Production host: Escherichia coli (E. coli) / Strain (production host): B834 / References: UniProt: P23526, adenosylhomocysteinase #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: 2.74 Å3/Da / Density % sol: 55.11 % |
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Crystal grow | pH: 5.6 / Details: pH 5.6 |
Crystal grow | *PLUS Method: unknown |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X12C / Wavelength: 0.95 |
Detector | Type: BRANDEIS / Detector: CCD / Date: Jul 1, 1997 |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.95 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→50 Å / Num. obs: 50613 / % possible obs: 99.5 % / Redundancy: 6.9 % / Biso Wilson estimate: 28 Å2 / Rmerge(I) obs: 0.074 / Net I/σ(I): 11.5 |
Reflection shell | Resolution: 2.8→2.9 Å / % possible all: 99.5 |
Reflection | *PLUS Num. measured all: 350530 |
Reflection shell | *PLUS % possible obs: 99.5 % |
-Processing
Software |
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Refinement | Method to determine structure: SAS / Resolution: 2.8→20 Å / Rfactor Rfree error: 0.004 / Data cutoff high rms absF: 5838962.45 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
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Solvent computation | Solvent model: FLAT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 21.8 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.8→20 Å
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Refine LS restraints |
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Refine LS restraints NCS | NCS model details: RESTRAINTS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.8→2.97 Å / Rfactor Rfree error: 0.012 / Total num. of bins used: 6
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Xplor file |
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Software | *PLUS Name: CNS / Version: 0.1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor obs: 0.311 |