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- PDB-7khm: Crystal structure of hDHHS20 bound to palmitoyl CoA -

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Basic information

Entry
Database: PDB / ID: 7khm
TitleCrystal structure of hDHHS20 bound to palmitoyl CoA
ComponentsIsoform 4 of Palmitoyltransferase ZDHHC20
KeywordsMEMBRANE PROTEIN / TRANSFERASE / 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
Palmitoyl-CoA / PHOSPHATE ION / Palmitoyltransferase ZDHHC20
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.88 Å
AuthorsLee, C.-J. / Banerjee, A.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2022
Title: Bivalent recognition of fatty acyl-CoA by a human integral membrane palmitoyltransferase.
Authors: Lee, C.J. / Stix, R. / Rana, M.S. / Shikwana, F. / Murphy, R.E. / Ghirlando, R. / Faraldo-Gomez, J.D. / Banerjee, A.
History
DepositionOct 21, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 2, 2022Provider: repository / Type: Initial release
Revision 1.1Feb 23, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Isoform 4 of Palmitoyltransferase ZDHHC20
B: Isoform 4 of Palmitoyltransferase ZDHHC20
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,3579
Polymers76,9892
Non-polymers2,3687
Water25214
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: equilibrium centrifugation
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1530 Å2
ΔGint-16 kcal/mol
Surface area28210 Å2
Unit cell
Length a, b, c (Å)53.529, 114.610, 83.596
Angle α, β, γ (deg.)90.000, 91.230, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Isoform 4 of Palmitoyltransferase ZDHHC20 / Acyltransferase ZDHHC20 / DHHC domain-containing cysteine-rich protein 20 / DHHC20 / Zinc finger ...Acyltransferase ZDHHC20 / DHHC domain-containing cysteine-rich protein 20 / DHHC20 / Zinc finger DHHC domain-containing protein 20


Mass: 38494.324 Da / Num. of mol.: 2 / Mutation: C156S
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 , Transferases; Acyltransferases; Transferring groups other than aminoacyl groups
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-PKZ / Palmitoyl-CoA / Palmitoyl-CoA


Mass: 1005.943 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C37H66N7O17P3S / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 14 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 63.06 %
Crystal growTemperature: 293 K / Method: lipidic cubic phase
Details: 50mM MES, pH 6.5, 50mM NaH2PO4, 30.3% PEG 300, 50mM DTT, 2.5% 2,5-hexanediol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 0.97918 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 17, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.88→83.58 Å / Num. obs: 22858 / % possible obs: 99.7 % / Redundancy: 6.9 % / CC1/2: 0.999 / Rmerge(I) obs: 0.163 / Rpim(I) all: 0.067 / Rrim(I) all: 0.176 / Net I/σ(I): 7.6 / Num. measured all: 158295
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.88-3.047.13.3292352433300.4361.3473.5950.699.6
9.11-83.586.70.04750457490.9990.020.05234.999.5

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation5.77 Å67.45 Å
Translation5.77 Å67.45 Å

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Processing

Software
NameVersionClassification
PHENIX1.82refinement
XDS20180808data reduction
Aimless0.5.32data scaling
PHASER2.8.3phasing
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6BMM

6bmm


Resolution: 2.88→67.53 Å / SU ML: 0.56 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 44.85 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3245 1974 8.9 %
Rwork0.2938 20218 -
obs0.2964 22192 96.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 266.98 Å2 / Biso mean: 129.9206 Å2 / Biso min: 87.49 Å2
Refinement stepCycle: final / Resolution: 2.88→67.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4517 0 105 14 4636
Biso mean--142.11 112.28 -
Num. residues----577
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0034800
X-RAY DIFFRACTIONf_angle_d0.4966561
X-RAY DIFFRACTIONf_dihedral_angle_d12.7691573
X-RAY DIFFRACTIONf_chiral_restr0.036713
X-RAY DIFFRACTIONf_plane_restr0.003787
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.88-2.950.62551100.57641092120273
2.95-3.030.58261350.56221369150493
3.03-3.120.49791370.51821448158598
3.12-3.220.48341460.45741476162299
3.22-3.340.44291560.42611469162599
3.34-3.470.41441380.40671471160999
3.47-3.630.44141420.36051479162199
3.63-3.820.38011470.30761479162699
3.82-4.060.29481440.266214601604100
4.06-4.370.28621450.26891485163099
4.37-4.810.25821480.246914741622100
4.81-5.510.26011470.242915001647100
5.51-6.940.30051350.270915071642100
6.94-67.530.2811440.23281509165399
Refinement TLS params.Method: refined / Origin x: 6.6658 Å / Origin y: 0.2702 Å / Origin z: 19.7347 Å
111213212223313233
T0.9431 Å2-0.0088 Å20.0165 Å2-1.1009 Å20.0114 Å2--1.0328 Å2
L0.036 °20.4048 °2-0.044 °2-1.8935 °20.1991 °2---0.0265 °2
S0.0346 Å °-0.0237 Å °0.0135 Å °-0.1735 Å °-0.0847 Å °-0.0806 Å °-0.1265 Å °-0.0428 Å °-0.0001 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA7 - 501
2X-RAY DIFFRACTION1allB10 - 501
3X-RAY DIFFRACTION1allC1 - 27
4X-RAY DIFFRACTION1allD1

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