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Yorodumi- PDB-7thn: Crystal structure of PigI trapped with PigG using a proline adeno... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7thn | ||||||||||||
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Title | Crystal structure of PigI trapped with PigG using a proline adenosine vinylsulfonamide inhibitor | ||||||||||||
Components |
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Keywords | LIGASE / nonribosomal peptide synthetase / NRPS / type II / biosynthesis / Ligase-Transport protein complex | ||||||||||||
Function / homology | Function and homology information L-proline-[L-prolyl-carrier protein] ligase / ligase activity / antibiotic biosynthetic process / ATP binding Similarity search - Function | ||||||||||||
Biological species | Serratia sp. ATCC 39006 (bacteria) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å | ||||||||||||
Authors | Corpuz, J.C. / Podust, L.M. | ||||||||||||
Funding support | United States, 3items
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Citation | Journal: Acs Chem.Biol. / Year: 2022 Title: Essential Role of Loop Dynamics in Type II NRPS Biomolecular Recognition. Authors: Corpuz, J.C. / Patel, A. / Davis, T.D. / Podust, L.M. / McCammon, J.A. / Burkart, M.D. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7thn.cif.gz | 142.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7thn.ent.gz | 104.2 KB | Display | PDB format |
PDBx/mmJSON format | 7thn.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/th/7thn ftp://data.pdbj.org/pub/pdb/validation_reports/th/7thn | HTTPS FTP |
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-Related structure data
Related structure data | 7thqC 6o6eS 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 , 2 types, 2 molecules BE
#1: Protein | Mass: 54823.832 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Serratia sp. ATCC 39006 (bacteria) / Strain: ATCC 39006 / Gene: pigI / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 References: UniProt: Q5W263, L-proline-[L-prolyl-carrier protein] ligase |
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#2: Protein | Mass: 10689.031 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Serratia sp. ATCC 39006 (bacteria) / Strain: ATCC 39006 / Gene: pigG / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q5W265 |
-Non-polymers , 5 types, 639 molecules
#3: Chemical | ChemComp-GOL / | ||||||
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#4: Chemical | ChemComp-AZI / #5: Chemical | ChemComp-MG / | #6: Chemical | ChemComp-I5M / | #7: Water | ChemComp-HOH / | |
-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: 2.24 Å3/Da / Density % sol: 45.11 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.23 Details: 0.3 M MgCl2, 24.57% PEG 3350, and 0.1 M BIS-TRIS pH 6.23 |
-Data collection
Diffraction | Mean temperature: 110 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.12 Å |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Aug 16, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.12 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→62.55 Å / Num. obs: 510902 / % possible obs: 99.92 % / Redundancy: 6.8 % / CC1/2: 0.998 / CC star: 1 / Rmerge(I) obs: 0.1141 / Rpim(I) all: 0.04718 / Rrim(I) all: 0.1237 / Net I/σ(I): 12.66 |
Reflection shell | Resolution: 1.6→1.662 Å / Redundancy: 6.2 % / Rmerge(I) obs: 1.045 / Mean I/σ(I) obs: 1.62 / Num. unique obs: 7504 / CC1/2: 0.603 / CC star: 0.867 / Rpim(I) all: 0.4542 / Rrim(I) all: 1.142 / % possible all: 99.93 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6o6e Resolution: 1.6→62.55 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.956 / SU B: 1.763 / SU ML: 0.06 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.077 / ESU R Free: 0.08 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 73.1 Å2 / Biso mean: 17.858 Å2 / Biso min: 8.29 Å2
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Refinement step | Cycle: final / Resolution: 1.6→62.55 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.605→1.646 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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