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Yorodumi- PDB-7yq1: Crystal structure of adenosine 5'-phosphosulfate kinase from Arch... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7yq1 | ||||||
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Title | Crystal structure of adenosine 5'-phosphosulfate kinase from Archaeoglobus fulgidus in complex with AMP-PNP and APS | ||||||
Components | Adenylyl-sulfate kinase | ||||||
Keywords | TRANSFERASE / APS kinase / archaea | ||||||
Function / homology | Function and homology information adenylyl-sulfate kinase / adenylylsulfate kinase activity / sulfate assimilation / hydrogen sulfide biosynthetic process / phosphorylation / ATP binding Similarity search - Function | ||||||
Biological species | Archaeoglobus fulgidus (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.91 Å | ||||||
Authors | Kawakami, T. / Teramoto, T. / Kakuta, Y. | ||||||
Funding support | Japan, 1items
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Citation | Journal: Biochem.Biophys.Res.Commun. / Year: 2022 Title: Crystal structure of adenosine 5'-phosphosulfate kinase isolated from Archaeoglobus fulgidus. Authors: Kawakami, T. / Teramoto, T. / Kakuta, Y. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7yq1.cif.gz | 479 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7yq1.ent.gz | 393.1 KB | Display | PDB format |
PDBx/mmJSON format | 7yq1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7yq1_validation.pdf.gz | 10.3 MB | Display | wwPDB validaton report |
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Full document | 7yq1_full_validation.pdf.gz | 10.4 MB | Display | |
Data in XML | 7yq1_validation.xml.gz | 55 KB | Display | |
Data in CIF | 7yq1_validation.cif.gz | 75.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yq/7yq1 ftp://data.pdbj.org/pub/pdb/validation_reports/yq/7yq1 | HTTPS FTP |
-Related structure data
Related structure data | 7yq0C 5cb6S S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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3 |
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Unit cell |
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Components on special symmetry positions |
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-Components
-Protein , 1 types, 6 molecules ABCDEF
#1: Protein | Mass: 20093.211 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Archaeoglobus fulgidus (archaea) / Gene: cysC, XD40_0245, XD48_1780 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A101DF63, adenylyl-sulfate kinase |
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-Non-polymers , 6 types, 967 molecules
#2: Chemical | ChemComp-ADX / #3: Chemical | ChemComp-ANP / #4: Chemical | ChemComp-MG / #5: Chemical | ChemComp-GOL / #6: Chemical | ChemComp-BO3 / #7: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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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: 3.44 Å3/Da / Density % sol: 64.29 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, hanging drop Details: 1.0 M Sodium citrate tribasic, 0.1 M Sodium cacodylate-hydrochloric acid |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL45XU / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 17, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.91→50 Å / Num. obs: 122344 / % possible obs: 98.3 % / Redundancy: 4.3 % / CC1/2: 0.987 / Net I/σ(I): 6 |
Reflection shell | Resolution: 1.91→2.03 Å / Num. unique obs: 20197 / CC1/2: 0.587 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5CB6 Resolution: 1.91→48.48 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 24.59 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.91→48.48 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: -3.7133 Å / Origin y: 1.0224 Å / Origin z: 28.4662 Å
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Refinement TLS group | Selection details: all |