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Yorodumi- PDB-8tn3: Structure of S. hygroscopicus aminotransferase MppQ complexed wit... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8tn3 | |||||||||
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Title | Structure of S. hygroscopicus aminotransferase MppQ complexed with pyridoxamine 5'-phosphate (PMP) | |||||||||
Components | PLP-dependent aminotransferase MppQ | |||||||||
Keywords | BIOSYNTHETIC PROTEIN / MANNOPEPTIMYCIN / AMINOTRANSFERASE / PMP | |||||||||
Function / homology | Function and homology information cellular biosynthetic process / transaminase activity / pyridoxal phosphate binding Similarity search - Function | |||||||||
Biological species | Streptomyces hygroscopicus (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.63 Å | |||||||||
Authors | Silvaggi, N.R. / Vuksanovic, N. | |||||||||
Funding support | United States, 1items
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Citation | Journal: Biochemistry / Year: 2023 Title: Structural and Biochemical Characterization of MppQ, an L-Enduracididine Biosynthetic Enzyme from Streptomyces hygroscopicus. Authors: Vuksanovic, N. / Melkonian, T.R. / Serrano, D.A. / Schwabacher, A.W. / Silvaggi, N.R. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8tn3.cif.gz | 452.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8tn3.ent.gz | 376.5 KB | Display | PDB format |
PDBx/mmJSON format | 8tn3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8tn3_validation.pdf.gz | 1 MB | Display | wwPDB validaton report |
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Full document | 8tn3_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | 8tn3_validation.xml.gz | 35.5 KB | Display | |
Data in CIF | 8tn3_validation.cif.gz | 54.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tn/8tn3 ftp://data.pdbj.org/pub/pdb/validation_reports/tn/8tn3 | HTTPS FTP |
-Related structure data
Related structure data | 8tn2C 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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Unit cell |
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-Components
#1: Protein | Mass: 44075.086 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptomyces hygroscopicus (bacteria) / Gene: mppQ / Plasmid: pE-SUMOkan / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q643B9 #2: Chemical | #3: Water | ChemComp-HOH / | 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: 2.14 Å3/Da / Density % sol: 42.58 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop Details: 15-25 % PEG 3350, and 0.1-0.2 M ammonium citrate trihydrate, trilithium citrate, or ammonium sulfate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97856 Å |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 8, 2010 |
Radiation | Monochromator: Si-111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97856 Å / Relative weight: 1 |
Reflection | Resolution: 1.63→43.09 Å / Num. obs: 89786 / % possible obs: 97.1 % / Redundancy: 3.9 % / Biso Wilson estimate: 14.95 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.078 / Rpim(I) all: 0.046 / Rrim(I) all: 0.09 / Χ2: 0.96 / Net I/σ(I): 9.91 |
Reflection shell | Resolution: 1.63→1.69 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.451 / Mean I/σ(I) obs: 3 / Num. unique obs: 8784 / CC1/2: 0.859 / Rpim(I) all: 0.262 / Rrim(I) all: 0.522 / Χ2: 0.96 / % possible all: 95.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.63→43.07 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / Phase error: 14.49 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.6 Å / VDW probe radii: 0.8 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.63→43.07 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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