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Yorodumi- PDB-1m7g: Crystal structure of APS kinase from Penicillium Chrysogenum: Ter... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1m7g | ||||||
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Title | Crystal structure of APS kinase from Penicillium Chrysogenum: Ternary structure with ADP and APS | ||||||
Components | Adenylylsulfate kinase | ||||||
Keywords | TRANSFERASE / APS kinase / Adenylylsulfate kinase / sulfate metabolism / Nucleotide 2 kinase | ||||||
Function / homology | Function and homology information 3'-phosphoadenosine 5'-phosphosulfate biosynthetic process / adenylyl-sulfate kinase / adenylylsulfate kinase activity / sulfate assimilation / hydrogen sulfide biosynthetic process / cysteine biosynthetic process / methionine biosynthetic process / phosphorylation / ATP binding / cytosol Similarity search - Function | ||||||
Biological species | Penicillium chrysogenum (fungus) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.43 Å | ||||||
Authors | Lansdon, E.B. / Segel, I.H. / Fisher, A.J. | ||||||
Citation | Journal: Biochemistry / Year: 2002 Title: Ligand-Induced Structural Changes in Adenosine 5'-Phosphosulfate Kinase from Penicillium chrysogenum. Authors: Lansdon, E.B. / Segel, I.H. / Fisher, A.J. | ||||||
History |
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Remark 999 | SEQUENCE Residue 54 in all of the subunits is listed as Arg in the database sequence (SwissProt ...SEQUENCE Residue 54 in all of the subunits is listed as Arg in the database sequence (SwissProt accession Q12657). According to the author, the gene has been resequenced and residue 54 is actually Gly. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1m7g.cif.gz | 190.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1m7g.ent.gz | 150.6 KB | Display | PDB format |
PDBx/mmJSON format | 1m7g.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1m7g_validation.pdf.gz | 3 MB | Display | wwPDB validaton report |
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Full document | 1m7g_full_validation.pdf.gz | 3.1 MB | Display | |
Data in XML | 1m7g_validation.xml.gz | 41.4 KB | Display | |
Data in CIF | 1m7g_validation.cif.gz | 59.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/m7/1m7g ftp://data.pdbj.org/pub/pdb/validation_reports/m7/1m7g | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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3 |
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4 |
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5 |
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Unit cell |
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-Components
-Protein , 1 types, 4 molecules ABCD
#1: Protein | Mass: 23804.781 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Penicillium chrysogenum (fungus) / Plasmid: pET23A / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q12657, adenylyl-sulfate kinase |
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-Non-polymers , 6 types, 806 molecules
#2: Chemical | ChemComp-SO4 / #3: Chemical | #4: Chemical | ChemComp-ADX / #5: Chemical | #6: Chemical | #7: 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: 2.48 Å3/Da / Density % sol: 50.32 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4 Details: Na monobasic phosphate, K dibasic phosphate, succinate, pH 4.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 8 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL9-1 / Wavelength: 0.97 Å |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Apr 26, 2001 |
Radiation | Monochromator: curved crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97 Å / Relative weight: 1 |
Reflection | Resolution: 1.43→30 Å / Num. all: 3135818 / Num. obs: 3135818 / % possible obs: 99.3 % / Observed criterion σ(I): -3 / Redundancy: 17.96 % / Biso Wilson estimate: 15.6 Å2 / Rmerge(I) obs: 0.049 / Rsym value: 0.049 / Net I/σ(I): 13.2 |
Reflection shell | Resolution: 1.43→1.45 Å / Rmerge(I) obs: 0.399 / Mean I/σ(I) obs: 4.5 / Num. unique all: 8523 / Rsym value: 0.399 / % possible all: 98 |
Reflection | *PLUS Lowest resolution: 30 Å / Num. obs: 174517 / Num. measured all: 3135818 |
Reflection shell | *PLUS % possible obs: 98 % |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 1.43→29.61 Å / Rfactor Rfree error: 0.002 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 42.472 Å2 / ksol: 0.394917 e/Å3 | |||||||||||||||||||||||||
Displacement parameters | Biso mean: 18.7 Å2
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Refine analyze | Luzzati coordinate error free: 0.17 Å / Luzzati sigma a free: 0.11 Å | |||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.43→29.61 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.43→1.52 Å / Rfactor Rfree error: 0.006 / Total num. of bins used: 6
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Xplor file |
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Refinement | *PLUS Lowest resolution: 30 Å / Num. reflection obs: 174517 / % reflection Rfree: 5 % / Rfactor Rwork: 0.18 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.24 |