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Yorodumi- PDB-8idw: Crystal structure of Fic protein from Mycoplasma mycoides in comp... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8idw | ||||||
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Title | Crystal structure of Fic protein from Mycoplasma mycoides in complex with AMPPNP | ||||||
Components | Cell filamentation protein Fic | ||||||
Keywords | TRANSFERASE / Fic protein / AMP transferase | ||||||
Function / homology | Fido-like domain superfamily / protein adenylyltransferase / Fic/DOC family / Fido domain / Fido domain profile. / transferase activity / AMP PHOSPHORAMIDATE / protein adenylyltransferase Function and homology information | ||||||
Biological species | Mycoplasma mycoides subsp. capri (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.304 Å | ||||||
Authors | Zhang, H. / Zhao, H.F. | ||||||
Funding support | China, 1items
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Citation | Journal: To Be Published Title: Crystal structure of Fic protein from Mycoplasma mycoides in complex with AMPPNP Authors: Zhang, H. / Zhao, H.F. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8idw.cif.gz | 167.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8idw.ent.gz | 133.6 KB | Display | PDB format |
PDBx/mmJSON format | 8idw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8idw_validation.pdf.gz | 3.1 MB | Display | wwPDB validaton report |
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Full document | 8idw_full_validation.pdf.gz | 3.2 MB | Display | |
Data in XML | 8idw_validation.xml.gz | 32.1 KB | Display | |
Data in CIF | 8idw_validation.cif.gz | 44.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/id/8idw ftp://data.pdbj.org/pub/pdb/validation_reports/id/8idw | HTTPS FTP |
-Related structure data
Similar structure data | Similarity search - Function & homologyF&H Search |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 22624.238 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycoplasma mycoides subsp. capri (bacteria) Gene: MMC68J_00751 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A7Z7PMX0 #2: Chemical | ChemComp-AN2 / #3: Chemical | ChemComp-MG / #4: Chemical | #5: 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: 2.64 Å3/Da / Density % sol: 53.38 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 0.2 M Magnesium chloride, 0.1 M BIS-TRIS, 25% w/v Polyethylene glycol 3,350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9785 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 5, 2022 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9785 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→50 Å / Num. obs: 41783 / % possible obs: 99.7 % / Redundancy: 35.9 % / Biso Wilson estimate: 37.1 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.074 / Rrim(I) all: 0.085 / Net I/σ(I): 11 |
Reflection shell | Resolution: 2.3→2.45 Å / Redundancy: 25.8 % / Rmerge(I) obs: 0.4 / Mean I/σ(I) obs: 2.8 / Num. unique obs: 6076 / CC1/2: 0.903 / Rrim(I) all: 0.479 / % possible all: 99.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.304→34.765 Å / SU ML: 0.3 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 30.69 / 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: 2.304→34.765 Å
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Refine LS restraints |
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LS refinement shell |
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