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- PDB-6bml: Structure of human DHHC20 palmitoyltransferase, irreversibly inhi... -

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Basic information

Entry
Database: PDB / ID: 6bml
TitleStructure of human DHHC20 palmitoyltransferase, irreversibly inhibited by 2-bromopalmitate
Componentshuman DHHC20 palmitoyltransferase
KeywordsTRANSFERASE / DHHC / lipid / acyl / palmitoyltransferase.
Function / homology
Function and homology information


protein-cysteine S-myristoyltransferase activity / protein-cysteine S-stearoyltransferase activity / peptidyl-L-cysteine S-palmitoylation / protein S-acyltransferase / protein palmitoylation / protein-cysteine S-palmitoyltransferase activity / palmitoyltransferase activity / synaptic vesicle maturation / positive regulation by host of viral process / protein targeting to membrane ...protein-cysteine S-myristoyltransferase activity / protein-cysteine S-stearoyltransferase activity / peptidyl-L-cysteine S-palmitoylation / protein S-acyltransferase / protein palmitoylation / protein-cysteine S-palmitoyltransferase activity / palmitoyltransferase activity / synaptic vesicle maturation / positive regulation by host of viral process / protein targeting to membrane / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups / endoplasmic reticulum-Golgi intermediate compartment membrane / Maturation of spike protein / Golgi membrane / intracellular membrane-bounded organelle / endoplasmic reticulum membrane / perinuclear region of cytoplasm / Golgi apparatus / endoplasmic reticulum / zinc ion binding / membrane / plasma membrane
Similarity search - Function
Palmitoyltransferase, DHHC domain / DHHC palmitoyltransferase / DHHC domain profile.
Similarity search - Domain/homology
3'-PHOSPHATE-ADENOSINE-5'-DIPHOSPHATE / PALMITIC ACID / PHOSPHATE ION / Palmitoyltransferase ZDHHC20
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.95 Å
AuthorsRana, M.S. / Lee, C.-J. / Banerjee, A.
CitationJournal: 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
DepositionNov 15, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 24, 2018Provider: repository / Type: Initial release
Revision 1.1Feb 21, 2018Group: Database references / Category: citation / Item: _citation.title
Revision 1.2Mar 28, 2018Group: Data collection / Database references / Category: citation / Item: _citation.title

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: human DHHC20 palmitoyltransferase
B: human DHHC20 palmitoyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,67211
Polymers69,2002
Non-polymers1,4729
Water543
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3590 Å2
ΔGint-25 kcal/mol
Surface area29720 Å2
Unit cell
Length a, b, c (Å)99.794, 99.794, 159.947
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number173
Space group name H-MP63

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein human DHHC20 palmitoyltransferase / Zinc finger DHHC domain-containing protein 20 / DHHC-20


Mass: 34600.133 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ZDHHC20 / Production host: Komagataella pastoris (fungus) / References: UniProt: Q5W0Z9, protein S-acyltransferase

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Non-polymers , 5 types, 12 molecules

#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-PLM / PALMITIC ACID / Palmitic acid


Mass: 256.424 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C16H32O2
#4: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#5: Chemical ChemComp-PAP / 3'-PHOSPHATE-ADENOSINE-5'-DIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O13P3
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.33 Å3/Da / Density % sol: 63.1 %
Crystal growTemperature: 293 K / Method: lipidic cubic phase
Details: 0.1M HEPES, pH 7.03, 50mM KH2PO4, 31% PEG 300, 50mM DTT, and 2.5% 2,5-hexanediol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.27951 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 12, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.27951 Å / Relative weight: 1
ReflectionResolution: 2.95→28.81 Å / Num. obs: 19027 / % possible obs: 99.9 % / Redundancy: 15.7 % / Biso Wilson estimate: 118.88 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.154 / Rpim(I) all: 0.04 / Rrim(I) all: 0.16 / Net I/σ(I): 13.6 / Num. measured all: 297993 / Scaling rejects: 0
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
2.95-3.1315.73.9330720.2841.014.05999.8
8.85-28.8114.70.04170910.0110.04297.1

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation6.28 Å28.81 Å
Translation6.28 Å28.81 Å

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Processing

Software
NameVersionClassification
PHENIX1.12_2829refinement
Aimless0.5.29data scaling
PHASER2.7.16phasing
PDB_EXTRACT3.22data extraction
Blu-Icedata collection
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.95→28.808 Å / SU ML: 0.44 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 28.12 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2453 1884 9.94 %
Rwork0.2356 --
obs0.2366 18958 99.75 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.95→28.808 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4772 0 81 3 4856
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0035029
X-RAY DIFFRACTIONf_angle_d0.4266811
X-RAY DIFFRACTIONf_dihedral_angle_d10.3662825
X-RAY DIFFRACTIONf_chiral_restr0.035729
X-RAY DIFFRACTIONf_plane_restr0.003823
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9505-3.03010.35211440.36551301X-RAY DIFFRACTION98
3.0301-3.11920.34121460.34621304X-RAY DIFFRACTION100
3.1192-3.21980.33561480.3361318X-RAY DIFFRACTION100
3.2198-3.33470.36721430.30261304X-RAY DIFFRACTION100
3.3347-3.4680.32971460.31011302X-RAY DIFFRACTION100
3.468-3.62550.30671480.2911292X-RAY DIFFRACTION100
3.6255-3.81630.22191400.27541324X-RAY DIFFRACTION100
3.8163-4.05480.29211430.25191315X-RAY DIFFRACTION100
4.0548-4.36680.25461400.2391317X-RAY DIFFRACTION100
4.3668-4.80450.26631510.22971321X-RAY DIFFRACTION100
4.8045-5.49550.2211430.221310X-RAY DIFFRACTION100
5.4955-6.90790.22981470.23881332X-RAY DIFFRACTION100
6.9079-28.80940.19371450.18331334X-RAY DIFFRACTION100

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