+Open data
-Basic information
Entry | Database: PDB / ID: 6bms | ||||||
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Title | Palmitoyltransferase structure | ||||||
Components | PalmitoyltransferasePalmitoyl-CoA | ||||||
Keywords | MEMBRANE PROTEIN / Membrane bound enzyme | ||||||
Function / homology | Function and homology information protein targeting to Golgi apparatus / peptidyl-L-cysteine S-palmitoylation / protein palmitoleylation / : / protein S-acyltransferase / protein-cysteine S-palmitoyltransferase activity / synaptic vesicle maturation / dopaminergic neuron differentiation / protein localization to membrane / protein targeting to membrane ...protein targeting to Golgi apparatus / peptidyl-L-cysteine S-palmitoylation / protein palmitoleylation / : / protein S-acyltransferase / protein-cysteine S-palmitoyltransferase activity / synaptic vesicle maturation / dopaminergic neuron differentiation / protein localization to membrane / protein targeting to membrane / forebrain development / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups / postsynaptic density / Golgi apparatus / endoplasmic reticulum / zinc ion binding Similarity search - Function | ||||||
Biological species | Danio rerio (zebrafish) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.441 Å | ||||||
Authors | Kumar, P. / Rajashankar, K. | ||||||
Funding support | United States, 1items
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Citation | Journal: Science / Year: 2018 Title: Fatty acyl recognition and transfer by an integral membraneS-acyltransferase. Authors: Rana, M.S. / Kumar, P. / Lee, C.J. / Verardi, R. / Rajashankar, K.R. / Banerjee, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6bms.cif.gz | 263 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6bms.ent.gz | 210 KB | Display | PDB format |
PDBx/mmJSON format | 6bms.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bm/6bms ftp://data.pdbj.org/pub/pdb/validation_reports/bm/6bms | HTTPS FTP |
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-Related 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
-Protein / Sugars , 2 types, 7 molecules AD
#1: Protein | Mass: 39683.902 Da / Num. of mol.: 2 / Mutation: C153S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Danio rerio (zebrafish) / Gene: zdhhc15b / Plasmid: pICZa-ZFDHHS15 / Production host: Komagataella phaffii GS115 (fungus) / References: UniProt: F1QXD3, protein S-acyltransferase #3: Sugar | ChemComp-LMT / |
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-Non-polymers , 5 types, 58 molecules
#2: Chemical | ChemComp-ZN / #4: Chemical | #5: Chemical | ChemComp-POV / ( | #6: Chemical | #7: Water | ChemComp-HOH / | |
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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: 5.1 Å3/Da / Density % sol: 75.99 % / Description: Diamond like |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: 100mM sodium cacodylate pH-5.5 100mM Sodium potassium tartrate 20% PEG400 PH range: 5.0-8.0 |
-Data collection
Diffraction | Mean temperature: 97 K / Ambient temp details: 97 |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 0.9797 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Jul 8, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9797 Å / Relative weight: 1 |
Reflection | Resolution: 2.44→50 Å / Num. obs: 58992 / % possible obs: 99.5 % / Redundancy: 9.1 % / Biso Wilson estimate: 55.98 Å2 / Rmerge(I) obs: 0.122 / Rpim(I) all: 0.042 / Rrim(I) all: 0.13 / Χ2: 1.107 / Net I/av σ(I): 17.66 / Net I/σ(I): 1.37 |
Reflection shell | Resolution: 2.44→2.49 Å / Redundancy: 9.1 % / Rmerge(I) obs: 1.176 / Mean I/σ(I) obs: 1.37 / Num. unique obs: 2697 / CC1/2: 0.225 / Rpim(I) all: 0.618 / Rrim(I) all: 1.339 / Χ2: 1.06 / % possible all: 92.6 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.441→37.213 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.51 / 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: 2.441→37.213 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: -47.0637 Å / Origin y: -1.4883 Å / Origin z: -24.89 Å
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Refinement TLS group | Selection details: all |