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Yorodumi- PDB-7vyp: The structure of GdmN complex with the natural tetrahedral interm... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7vyp | ||||||||||||||||||||||||
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Title | The structure of GdmN complex with the natural tetrahedral intermediate, carbamoylated derivative, and AMP | ||||||||||||||||||||||||
Components | GdmN | ||||||||||||||||||||||||
Keywords | TRANSFERASE / Carbamoylation / Ansamycins antibiotics / Homodimer | ||||||||||||||||||||||||
Function / homology | Function and homology information biosynthetic process / catalytic activity / ATP binding / metal ion binding Similarity search - Function | ||||||||||||||||||||||||
Biological species | Streptomyces hygroscopicus (bacteria) | ||||||||||||||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.88 Å | ||||||||||||||||||||||||
Authors | Wei, J. / Zheng, J. / Zhou, J. / Kang, Q. / Bai, L. | ||||||||||||||||||||||||
Funding support | 7items
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Citation | Journal: Nat Commun / Year: 2022 Title: Endowing homodimeric carbamoyltransferase GdmN with iterative functions through structural characterization and mechanistic studies. Authors: Wei, J. / Zhang, X. / Zhou, Y. / Cheng, X. / Lin, Z. / Tang, M. / Zheng, J. / Wang, B. / Kang, Q. / Bai, L. | ||||||||||||||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7vyp.cif.gz | 336.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7vyp.ent.gz | 217.9 KB | Display | PDB format |
PDBx/mmJSON format | 7vyp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vy/7vyp ftp://data.pdbj.org/pub/pdb/validation_reports/vy/7vyp | HTTPS FTP |
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-Related structure data
Related structure data | 7vx0C 7vyjC 7vyoC 7vznC 7vzqC 7vzuC 7vzyC 7vzzC 3venS 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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Unit cell |
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-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 74365.609 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptomyces hygroscopicus (bacteria) / Gene: gdmN / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q84G19 |
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-Non-polymers , 8 types, 94 molecules
#2: Chemical | #3: Chemical | ChemComp-SO4 / #4: Chemical | ChemComp-CP / | #5: Chemical | ChemComp-EDO / #6: Chemical | ChemComp-82Z / [( | #7: Chemical | ChemComp-AMP / | #8: Chemical | ChemComp-8CW / [( | #9: 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: 2.79 Å3/Da / Density % sol: 55.94 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, sitting drop Details: Lithium sulfate monohydrate, Polyethylene glycol 3,350, Tris |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.97853 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 2, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97853 Å / Relative weight: 1 |
Reflection | Resolution: 2.88→50 Å / Num. obs: 38176 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 9.8 % / Biso Wilson estimate: 49.6 Å2 / CC1/2: 0.989 / CC star: 0.997 / Rmerge(I) obs: 0.129 / Rpim(I) all: 0.043 / Rrim(I) all: 0.136 / Rsym value: 0.129 / Χ2: 0.907 / Net I/σ(I): 21.167 |
Reflection shell | Resolution: 2.88→2.93 Å / Num. unique obs: 1880 / CC1/2: 0.973 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3VEN Resolution: 2.88→27.76 Å / SU ML: 0.2955 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.1538 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 43.76 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.88→27.76 Å
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Refine LS restraints |
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LS refinement shell |
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