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Yorodumi- PDB-6i0p: Structure of quinolinate synthase in complex with 6-mercaptopyrid... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6i0p | ||||||
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Title | Structure of quinolinate synthase in complex with 6-mercaptopyridine-2,3-dicarboxylic acid | ||||||
Components | Quinolinate synthase A | ||||||
Keywords | TRANSFERASE / NAD BIOSYNTHESIS / IRON SULFUR CLUSTER | ||||||
Function / homology | Function and homology information 'de novo' NAD biosynthetic process from aspartate / quinolinate synthase / quinolinate synthetase A activity / 4 iron, 4 sulfur cluster binding / metal ion binding / cytosol Similarity search - Function | ||||||
Biological species | Thermotoga maritima (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 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 | 6i0p.cif.gz | 144 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6i0p.ent.gz | 111.5 KB | Display | PDB format |
PDBx/mmJSON format | 6i0p.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6i0p_validation.pdf.gz | 460.3 KB | Display | wwPDB validaton report |
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Full document | 6i0p_full_validation.pdf.gz | 460.8 KB | Display | |
Data in XML | 6i0p_validation.xml.gz | 16.4 KB | Display | |
Data in CIF | 6i0p_validation.cif.gz | 24.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/i0/6i0p ftp://data.pdbj.org/pub/pdb/validation_reports/i0/6i0p | HTTPS FTP |
-Related structure data
Related structure data | 6i0kC 6i0rC 6f48S C: citing same article (ref.) S: Starting model for refinement |
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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, Y21F Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermotoga maritima (strain ATCC 43589 / MSB8 / DSM 3109 / JCM 10099) (bacteria) Strain: ATCC 43589 / MSB8 / DSM 3109 / JCM 10099 / 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, 314 molecules
#2: Chemical | ChemComp-SF4 / |
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#3: Chemical | ChemComp-QAS / |
#4: Chemical | ChemComp-CL / |
#5: Chemical | ChemComp-PO4 / |
#6: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 2 |
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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: 7.3 / Details: PEG33500, dioxane, Na2HPO4, HEPES, anaerobic |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.97625 Å | ||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: May 21, 2017 | ||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97625 Å / Relative weight: 1 | ||||||||||||||||||||||||
Reflection | Resolution: 1.9→46.49 Å / Num. obs: 24522 / % possible obs: 99.7 % / Redundancy: 5.8 % / CC1/2: 0.995 / Rmerge(I) obs: 0.125 / Rpim(I) all: 0.055 / Rrim(I) all: 0.137 / Net I/σ(I): 9 / Num. measured all: 141788 / Scaling rejects: 2 | ||||||||||||||||||||||||
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: 1.9→46.49 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.954 / SU B: 8.79 / SU ML: 0.125 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.156 / ESU R Free: 0.133 Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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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: 92.02 Å2 / Biso mean: 34.929 Å2 / Biso min: 12.2 Å2
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Refinement step | Cycle: final / Resolution: 1.9→46.49 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.9→1.949 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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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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