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Yorodumi- PDB-6phr: Crystal structure of Marinobacter subterrani acetylpolyamine amid... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6phr | ||||||
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Title | Crystal structure of Marinobacter subterrani acetylpolyamine amidohydrolase (msAPAH) complexed with 5-[(3-aminopropyl)amino]pentane-1-thiol | ||||||
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: 1.65 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 | 6phr.cif.gz | 154.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6phr.ent.gz | 118.7 KB | Display | PDB format |
PDBx/mmJSON format | 6phr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6phr_validation.pdf.gz | 865.5 KB | Display | wwPDB validaton report |
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Full document | 6phr_full_validation.pdf.gz | 870.3 KB | Display | |
Data in XML | 6phr_validation.xml.gz | 28.1 KB | Display | |
Data in CIF | 6phr_validation.cif.gz | 40.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ph/6phr ftp://data.pdbj.org/pub/pdb/validation_reports/ph/6phr | HTTPS FTP |
-Related structure data
Related structure data | 6phtC 6phzC 6pi1C 6pi8C 6piaC 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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1 |
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Unit cell |
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-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 37980.547 Da / Num. of mol.: 2 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, 305 molecules
#2: Chemical | #3: Chemical | #4: Chemical | #5: Chemical | #6: Chemical | ChemComp-K / #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: 2.25 Å3/Da / Density % sol: 45.35 % / Description: Rod-like crystals |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, sitting drop Details: 10 mg/ml protein, 20% v/v-propanol, 0.1 MES monohydrate (pH 6.0), 20% w/v polyethylene glycol monomethyl ether 2000, 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: APS / Beamline: 24-ID-E / Wavelength: 0.98 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 14, 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: 1.65→61.77 Å / Num. obs: 79658 / % possible obs: 99.2 % / Redundancy: 6.1 % / Rpim(I) all: 0.106 / Net I/σ(I): 2.2 |
Reflection shell | Resolution: 1.65→1.68 Å / Num. unique obs: 7965 / Rpim(I) all: 0.675 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB 4ZUM Resolution: 1.65→61.765 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.15
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.65→61.765 Å
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Refine LS restraints |
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LS refinement shell |
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