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- PDB-1m7h: Crystal Structure of APS kinase from Penicillium Chrysogenum: Str... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1m7h | ||||||
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Title | Crystal Structure of APS kinase from Penicillium Chrysogenum: Structure with APS soaked out of one dimer | ||||||
![]() | Adenylylsulfate kinase | ||||||
![]() | TRANSFERASE / APS kinase / Adenylylsulfate kinase / sulfate metabolism / Nucleotide 2 kinase | ||||||
Function / homology | ![]() 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 | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Lansdon, E.B. / Sege, I.H. / Fisher, A.J. | ||||||
![]() | ![]() 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. |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 185.3 KB | Display | ![]() |
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PDB format | ![]() | 148.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 2.3 MB | Display | ![]() |
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Full document | ![]() | 2.3 MB | Display | |
Data in XML | ![]() | 39.6 KB | Display | |
Data in CIF | ![]() | 54.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
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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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Unit cell |
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Components
#1: Protein | Mass: 23804.781 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | ChemComp-SO4 / #3: Chemical | ChemComp-ADP / #4: Chemical | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.55 Å3/Da / Density % sol: 51.69 % | ||||||||||||||||||||||||||||||||||||||||||
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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, 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: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Jan 29, 2002 |
Radiation | Monochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 2→30 Å / Num. all: 621412 / Num. obs: 621412 / % possible obs: 97.3 % / Observed criterion σ(I): -3 / Redundancy: 9.61 % / Biso Wilson estimate: 20.4 Å2 / Rmerge(I) obs: 0.05 / Rsym value: 0.05 / Net I/σ(I): 14.1 |
Reflection shell | Resolution: 2→2.05 Å / Rmerge(I) obs: 0.329 / Mean I/σ(I) obs: 3.7 / Num. unique all: 4004 / Rsym value: 0.329 / % possible all: 91.5 |
Reflection | *PLUS Lowest resolution: 30 Å / Num. obs: 64678 / Num. measured all: 621412 / Rmerge(I) obs: 0.05 |
Reflection shell | *PLUS % possible obs: 91.5 % |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: Ternary structure of APS kinase Resolution: 2→29.91 Å / Rfactor Rfree error: 0.005 / 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: 54.4752 Å2 / ksol: 0.369587 e/Å3 | |||||||||||||||||||||||||
Displacement parameters | Biso mean: 38.4 Å2
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Refine analyze | Luzzati coordinate error free: 0.31 Å / Luzzati sigma a free: 0.25 Å | |||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→29.91 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.13 Å / Rfactor Rfree error: 0.014 / 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: 64678 / % reflection Rfree: 5 % | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
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