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Yorodumi- PDB-4utv: Crystal structure of zebrafish Sirtuin 5 in complex with 3-phenyl... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4utv | ||||||
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Title | Crystal structure of zebrafish Sirtuin 5 in complex with 3-phenyl- succinylated CPS1-peptide | ||||||
Components |
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Keywords | HYDROLASE / REGULATORY ENZYME / DEACYLASE / MITOCHONDRIAL / ROSSMANN-FOLD / ZINC-BINDING | ||||||
Function / homology | Function and homology information carbamoyl phosphate biosynthetic process / cellular response to oleic acid / Transcriptional activation of mitochondrial biogenesis / monoatomic anion homeostasis / regulation of ketone biosynthetic process / peptidyl-lysine demalonylation / protein desuccinylation / peptidyl-lysine desuccinylation / protein-glutaryllysine deglutarylase activity / triglyceride catabolic process ...carbamoyl phosphate biosynthetic process / cellular response to oleic acid / Transcriptional activation of mitochondrial biogenesis / monoatomic anion homeostasis / regulation of ketone biosynthetic process / peptidyl-lysine demalonylation / protein desuccinylation / peptidyl-lysine desuccinylation / protein-glutaryllysine deglutarylase activity / triglyceride catabolic process / modified amino acid binding / protein-malonyllysine demalonylase activity / protein-succinyllysine desuccinylase activity / carbamoyl-phosphate synthase (ammonia) / carbamoyl-phosphate synthase (ammonia) activity / carbamoyl-phosphate synthase (glutamine-hydrolyzing) activity / midgut development / homocysteine metabolic process / cellular response to ammonium ion / Urea cycle / citrulline biosynthetic process / urea cycle / hepatocyte differentiation / NAD-dependent histone deacetylase activity / cellular response to fibroblast growth factor stimulus / response to growth hormone / response to food / glutamate binding / nitric oxide metabolic process / response to zinc ion / heterocyclic compound binding / glutamine metabolic process / response to dexamethasone / cellular response to glucagon stimulus / response to starvation / mitochondrial nucleoid / response to amine / small molecule binding / potassium ion binding / acyl binding / NAD+ binding / response to amino acid / 'de novo' pyrimidine nucleobase biosynthetic process / cellular response to cAMP / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups / vasodilation / response to toxic substance / phospholipid binding / endopeptidase activity / transferase activity / response to lipopolysaccharide / mitochondrial inner membrane / mitochondrial matrix / response to xenobiotic stimulus / calcium ion binding / protein-containing complex binding / nucleolus / protein-containing complex / mitochondrion / zinc ion binding / ATP binding / nucleus / metal ion binding / plasma membrane / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | DANIO RERIO (zebrafish) HOMO SAPIENS (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å | ||||||
Authors | Pannek, M. / Gertz, M. / Steegborn, C. | ||||||
Citation | Journal: Angew.Chem.Int.Ed.Engl. / Year: 2014 Title: Chemical Probing of the Human Sirtuin 5 Active Site Reveals its Substrate Acyl Specificity and Peptide-Based Inhibitors. Authors: Roessler, C. / Nowak, T. / Pannek, M. / Gertz, M. / Nguyen, G.T. / Scharfe, M. / Born, I. / Sippl, W. / Steegborn, C. / Schutkowski, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4utv.cif.gz | 219.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4utv.ent.gz | 177.1 KB | Display | PDB format |
PDBx/mmJSON format | 4utv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4utv_validation.pdf.gz | 495 KB | Display | wwPDB validaton report |
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Full document | 4utv_full_validation.pdf.gz | 501.9 KB | Display | |
Data in XML | 4utv_validation.xml.gz | 22.8 KB | Display | |
Data in CIF | 4utv_validation.cif.gz | 32 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ut/4utv ftp://data.pdbj.org/pub/pdb/validation_reports/ut/4utv | HTTPS FTP |
-Related structure data
Related structure data | 4utnC 4utrC 4utxC 4utzC 4uu7C 4uu8C 4uuaC 4uubC 2nyrS 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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2 |
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Unit cell |
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Components on special symmetry positions |
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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (-0.82161, -0.46688, -0.32707), Vector: |
-Components
-Protein / Protein/peptide , 2 types, 3 molecules ABC
#1: Protein | Mass: 30423.785 Da / Num. of mol.: 2 / Fragment: CATALYTIC CORE, RESIDUES 30-298 Source method: isolated from a genetically manipulated source Source: (gene. exp.) DANIO RERIO (zebrafish) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): CODONPLUS References: UniProt: Q6DHI5, Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds; In linear amides #2: Protein/peptide | | Mass: 969.112 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 524-531 / Source method: obtained synthetically / Source: (synth.) HOMO SAPIENS (human) / References: UniProt: Q5R209, UniProt: P31327*PLUS |
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-Non-polymers , 7 types, 141 molecules
#3: Chemical | #4: Chemical | ChemComp-EPE / | #5: Chemical | ChemComp-DMS / | #6: Chemical | ChemComp-NA / | #7: Chemical | ChemComp-FSL / ( | #8: Chemical | ChemComp-F9V / ( | #9: Water | ChemComp-HOH / | |
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-Details
Sequence details | N-TERMINAL RESIDUES GIDPFT ARE ENCODED ON THE PET151 VECTOR AND DO NOT BELONG TO THE NATURAL ...N-TERMINAL RESIDUES GIDPFT ARE ENCODED ON THE PET151 VECTOR AND DO NOT BELONG TO THE NATURAL ZEBRAFISH SIRT5 PROTEIN |
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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: 2.9 Å3/Da / Density % sol: 57 % / Description: NONE |
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Crystal grow | pH: 7.6 / Details: 22% PEG3350, 0.1 M HEPES PH 7.6 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.918 |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 14, 2012 / Details: MIRROR |
Radiation | Monochromator: SI111 CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.918 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→100 Å / Num. obs: 28997 / % possible obs: 99.9 % / Observed criterion σ(I): 2 / Redundancy: 7.1 % / Rmerge(I) obs: 0.12 / Net I/σ(I): 14.4 |
Reflection shell | Resolution: 2.4→2.46 Å / Redundancy: 7.3 % / Rmerge(I) obs: 1.2 / Mean I/σ(I) obs: 1.94 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2NYR Resolution: 2.4→47.85 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.942 / SU B: 14.892 / SU ML: 0.171 / Cross valid method: THROUGHOUT / ESU R: 0.314 / ESU R Free: 0.22 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED. STRUCTURE WAS REFINED USING PROSMART WITH PDB-ID 3RIY R.A. NICHOLLS, F. LONG AND G.N. MURSHUDOV 2012 LOW ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED. STRUCTURE WAS REFINED USING PROSMART WITH PDB-ID 3RIY R.A. NICHOLLS, F. LONG AND G.N. MURSHUDOV 2012 LOW RESOLUTION REFINEMENT TOOLS IN REFMAC5. ACTA CRYST. D. MISSING N-TERMINAL RESIDUES ARE DISORDERED RESIDUES A275 TO A281 ARE DISORDERED RESIDUES B274 TO B280 ARE DISORDERED
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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 mean: 44.052 Å2
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Refinement step | Cycle: LAST / Resolution: 2.4→47.85 Å
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Refine LS restraints |
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