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Yorodumi- PDB-6i0k: Structure of quinolinate synthase in complex with 4-mercaptophtha... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6i0k | ||||||
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Title | Structure of quinolinate synthase in complex with 4-mercaptophthalic acid | ||||||
Components | Quinolinate synthase A | ||||||
Keywords | TRANSFERASE / NAD BIOSYNTHESIS / IRON SULFUR CLUSTER | ||||||
Function / homology | Function and homology information quinolinate synthase / quinolinate synthetase A activity / 'de novo' NAD biosynthetic process from aspartate / 4 iron, 4 sulfur cluster binding / metal ion binding / cytosol Similarity search - Function | ||||||
Biological species | Thermotoga maritima MSB8 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.64 Å | ||||||
Authors | Volbeda, A. / Fontecilla-Camps, J.C. | ||||||
Funding support | France, 1items
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Citation | Journal: Chem.Commun.(Camb.) / Year: 2019 Title: Design of specific inhibitors of quinolinate synthase based on [4Fe-4S] cluster coordination. Authors: Saez Cabodevilla, J. / Volbeda, A. / Hamelin, O. / Latour, J.M. / Gigarel, O. / Clemancey, M. / Darnault, C. / Reichmann, D. / Amara, P. / Fontecilla-Camps, J.C. / Ollagnier de Choudens, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6i0k.cif.gz | 148.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6i0k.ent.gz | 114.6 KB | Display | PDB format |
PDBx/mmJSON format | 6i0k.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/i0/6i0k ftp://data.pdbj.org/pub/pdb/validation_reports/i0/6i0k | HTTPS FTP |
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-Related structure data
Related structure data | 6i0pC 6i0rC 6f48S 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, 1 molecules A
#1: Protein | Mass: 34640.598 Da / Num. of mol.: 1 / Mutation: K219R Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermotoga maritima MSB8 (bacteria) / Gene: nadA, TM_1644 / Plasmid: PT7 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9X1X7, quinolinate synthase |
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-Non-polymers , 5 types, 271 molecules
#2: Chemical | ChemComp-SF4 / |
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#3: Chemical | ChemComp-GZ8 / |
#4: Chemical | ChemComp-PO4 / |
#5: Chemical | ChemComp-CL / |
#6: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.28 Å3/Da / Density % sol: 46.13 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion / pH: 7 / Details: PEG33500, NaCl, Na2HPO4, MES, anaerobic |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 1.07438 Å | ||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Aug 17, 2016 | ||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.07438 Å / Relative weight: 1 | ||||||||||||||||||||||||
Reflection | Resolution: 1.6→46.8 Å / Num. obs: 40160 / % possible obs: 98.7 % / Redundancy: 4.4 % / CC1/2: 0.997 / Rmerge(I) obs: 0.085 / Rpim(I) all: 0.045 / Rrim(I) all: 0.096 / Net I/σ(I): 8.7 / Num. measured all: 176966 / Scaling rejects: 15 | ||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6F48 Resolution: 1.64→46.8 Å / Cor.coef. Fo:Fc: 0.978 / Cor.coef. Fo:Fc free: 0.962 / SU B: 6.584 / SU ML: 0.094 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.131 / ESU R Free: 0.096 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 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 92.15 Å2 / Biso mean: 32.414 Å2 / Biso min: 18.98 Å2
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Refinement step | Cycle: final / Resolution: 1.64→46.8 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.64→1.683 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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