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Yorodumi- PDB-6pia: Crystal structure of Marinobacter subterrani acetylpolyamine amid... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6pia | ||||||
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Title | Crystal structure of Marinobacter subterrani acetylpolyamine amidohydrolase (msAPAH) complexed with 6-[(3-aminopropyl)amino]-N-hydroxyhexanamide | ||||||
Components | Acetylpolyamine amidohydrolase | ||||||
Keywords | HYDROLASE/INHIBITOR / acetylpolyamine amidohydrolase / polyamine deacetylase / hydrolase / hydrolase inhibitor / HYDROLASE-INHIBITOR complex | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Marinobacter subterrani (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å | ||||||
Authors | Osko, J.D. / Christianson, D.W. | ||||||
Funding support | United States, 1items
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Citation | Journal: Biochemistry / Year: 2019 Title: Structure and Function of the Acetylpolyamine Amidohydrolase from the Deep Earth HalophileMarinobacter subterrani. Authors: Osko, J.D. / Roose, B.W. / Shinsky, S.A. / Christianson, D.W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6pia.cif.gz | 295.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6pia.ent.gz | 234.3 KB | Display | PDB format |
PDBx/mmJSON format | 6pia.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6pia_validation.pdf.gz | 1.2 MB | Display | wwPDB validaton report |
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Full document | 6pia_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | 6pia_validation.xml.gz | 55.7 KB | Display | |
Data in CIF | 6pia_validation.cif.gz | 80.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pi/6pia ftp://data.pdbj.org/pub/pdb/validation_reports/pi/6pia | HTTPS FTP |
-Related structure data
Related structure data | 6phrC 6phtC 6phzC 6pi1C 6pi8C 6picC 6pidC 4zumS 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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-Components
-Protein , 1 types, 4 molecules ABCD
#1: Protein | Mass: 37980.547 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Marinobacter subterrani (bacteria) / Gene: Msub_13096 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0J7JFD7 |
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-Non-polymers , 6 types, 788 molecules
#2: Chemical | ChemComp-ZN / #3: Chemical | ChemComp-K / #4: Chemical | ChemComp-MG / #5: Chemical | #6: Chemical | ChemComp-XS6 / #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: 2.31 Å3/Da / Density % sol: 46.85 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop Details: 10 mg/ml msAPAH Protein, 0.2 M calcium chloride dihydrate, 20% w/v PEG 3350, 1:1 ratio protein to precipitant |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.98 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 22, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 1.75→46.27 Å / Num. obs: 131376 / % possible obs: 95.6 % / Redundancy: 3.2 % / Rpim(I) all: 0.085 / Net I/σ(I): 7.3 |
Reflection shell | Resolution: 1.75→1.81 Å / Num. unique obs: 12851 / Rpim(I) all: 0.47 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB: 4ZUM Resolution: 1.75→46.27 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.05
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.75→46.27 Å
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Refine LS restraints |
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LS refinement shell |
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