+Open data
-Basic information
Entry | Database: PDB / ID: 5d6j | ||||||
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Title | Crystal structure of a mycobacterial protein | ||||||
Components |
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Keywords | LIGASE/PROTEIN BINDING / Mycobacterium smegmatis / LIGASE-PROTEIN BINDING complex | ||||||
Function / homology | Function and homology information long-chain-fatty-acid-[acyl-carrier-protein] ligase / long-chain fatty acid [acyl-carrier-protein] ligase activity / SUMO is conjugated to E1 (UBA2:SAE1) / SUMOylation of nuclear envelope proteins / SUMO is transferred from E1 to E2 (UBE2I, UBC9) / SUMO is proteolytically processed / SUMOylation of transcription factors / Postmitotic nuclear pore complex (NPC) reformation / SUMOylation of transcription cofactors / SUMOylation of DNA damage response and repair proteins ...long-chain-fatty-acid-[acyl-carrier-protein] ligase / long-chain fatty acid [acyl-carrier-protein] ligase activity / SUMO is conjugated to E1 (UBA2:SAE1) / SUMOylation of nuclear envelope proteins / SUMO is transferred from E1 to E2 (UBE2I, UBC9) / SUMO is proteolytically processed / SUMOylation of transcription factors / Postmitotic nuclear pore complex (NPC) reformation / SUMOylation of transcription cofactors / SUMOylation of DNA damage response and repair proteins / SUMOylation of DNA replication proteins / septin ring / SUMOylation of SUMOylation proteins / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / SUMOylation of RNA binding proteins / SUMOylation of chromatin organization proteins / lipid biosynthetic process / ubiquitin-like protein ligase binding / protein sumoylation / fatty acid metabolic process / condensed nuclear chromosome / PML body / protein tag activity / ATP binding / identical protein binding / nucleus Similarity search - Function | ||||||
Biological species | Mycobacterium smegmatis (bacteria) Saccharomyces cerevisiae (brewer's yeast) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 Å | ||||||
Authors | Li, W.J. / Bi, L.J. | ||||||
Funding support | China, 1items
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Citation | Journal: Sci Rep / Year: 2015 Title: Crystal structure of FadD32, an enzyme essential for mycolic acid biosynthesis in mycobacteria. Authors: Li, W. / Gu, S. / Fleming, J. / Bi, L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5d6j.cif.gz | 163.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5d6j.ent.gz | 123.5 KB | Display | PDB format |
PDBx/mmJSON format | 5d6j.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/d6/5d6j ftp://data.pdbj.org/pub/pdb/validation_reports/d6/5d6j | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 68306.500 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria) Strain: ATCC 700084 / mc(2)155 / Gene: fadD32, MSMEG_6393, MSMEI_6225 / Production host: Escherichia coli (E. coli) / References: UniProt: A0R618 |
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#2: Protein | Mass: 8696.812 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 21-94 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Strain: ATCC 204508 / S288c / Gene: SMT3, YDR510W, D9719.15 / Production host: Escherichia coli (E. coli) / References: UniProt: Q12306 |
#3: Chemical | ChemComp-MG / |
#4: Chemical | ChemComp-ATP / |
#5: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 3.46 Å3/Da / Density % sol: 64.42 % |
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Crystal grow | Temperature: 281 K / Method: evaporation / Details: 0.2 M sodium malonate, 20% PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.97928 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 7, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97928 Å / Relative weight: 1 |
Reflection | Resolution: 2.25→50 Å / % possible obs: 100 % / Redundancy: 14.3 % / Rmerge(I) obs: 0.099 / Net I/σ(I): 26.5 |
Reflection shell | Resolution: 2.25→2.33 Å / Redundancy: 14.8 % / Rmerge(I) obs: 0.557 / Mean I/σ(I) obs: 6.2 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.25→29.985 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.88 / 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: 2.25→29.985 Å
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Refine LS restraints |
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LS refinement shell |
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