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- PDB-6bmm: Structure of human DHHC20 palmitoyltransferase, space group P21 -

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Basic information

Entry
Database: PDB / ID: 6bmm
TitleStructure of human DHHC20 palmitoyltransferase, space group P21
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 / endoplasmic reticulum / Golgi apparatus / zinc ion binding / membrane / plasma membrane
Similarity search - Function
Palmitoyltransferase ZDHHC16 / Palmitoyltransferase, DHHC domain / DHHC palmitoyltransferase / DHHC domain profile.
Similarity search - Domain/homology
(2S,5S)-hexane-2,5-diol / (2S)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / PHOSPHATE ION / Palmitoyltransferase ZDHHC20
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.35 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
Revision 1.3Oct 23, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_conn_type / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn_type.id / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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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)70,86216
Polymers68,9882
Non-polymers1,87414
Water93752
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area740 Å2
ΔGint-10 kcal/mol
Surface area28720 Å2
Unit cell
Length a, b, c (Å)86.519, 57.700, 94.098
Angle α, β, γ (deg.)90.000, 115.510, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and ((resid 8 through 9 and (name N...
21(chain B and (resid 8 through 9 or (resid 12...

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ARGARGCYSCYS(chain A and ((resid 8 through 9 and (name N...AA8 - 92 - 3
12TRPTRPLEULEU(chain A and ((resid 8 through 9 and (name N...AA7 - 2961 - 290
13TRPTRPLEULEU(chain A and ((resid 8 through 9 and (name N...AA7 - 2961 - 290
14TRPTRPLEULEU(chain A and ((resid 8 through 9 and (name N...AA7 - 2961 - 290
15TRPTRPLEULEU(chain A and ((resid 8 through 9 and (name N...AA7 - 2961 - 290
21ARGARGCYSCYS(chain B and (resid 8 through 9 or (resid 12...BB8 - 92 - 3
22ARGARGVALVAL(chain B and (resid 8 through 9 or (resid 12...BB12 - 146 - 8
23ARGARGVALVAL(chain B and (resid 8 through 9 or (resid 12...BB8 - 2972 - 291
24ARGARGVALVAL(chain B and (resid 8 through 9 or (resid 12...BB8 - 2972 - 291
25ARGARGVALVAL(chain B and (resid 8 through 9 or (resid 12...BB8 - 2972 - 291
26ARGARGVALVAL(chain B and (resid 8 through 9 or (resid 12...BB8 - 2972 - 291

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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: 34494.051 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, 66 molecules

#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#4: Chemical ChemComp-OLB / (2S)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate


Mass: 356.540 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H40O4
#5: Chemical
ChemComp-DYD / (2S,5S)-hexane-2,5-diol


Mass: 118.174 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C6H14O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 52 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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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: 3.1 Å3/Da / Density % sol: 60.31 %
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
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.27951 Å
DetectorType: DECTRIS PILATUS3 S 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: 2.35→28.85 Å / Num. obs: 35217 / % possible obs: 99.9 % / Redundancy: 8.2 % / Biso Wilson estimate: 63.12 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.12 / Rpim(I) all: 0.045 / Rrim(I) all: 0.129 / Net I/σ(I): 10 / Num. measured all: 287546 / Scaling rejects: 0
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
2.35-2.448.22.20136330.3870.8062.34999.5
8.79-28.857.30.0537020.9990.0210.05897

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation4.75 Å28.85 Å
Translation4.75 Å28.85 Å

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Processing

Software
NameVersionClassification
Aimless0.5.27data scaling
PHASER2.7.15phasing
PHENIX1.12_2829refinement
PDB_EXTRACT3.22data extraction
XDSdata reduction
Blu-Icedata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.35→28.85 Å / SU ML: 0.38 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 31.99
RfactorNum. reflection% reflection
Rfree0.2603 1988 5.66 %
Rwork0.2413 --
obs0.2424 35135 99.73 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 264.95 Å2 / Biso mean: 80.2945 Å2 / Biso min: 43.17 Å2
Refinement stepCycle: final / Resolution: 2.35→28.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4538 0 112 52 4702
Biso mean--89.89 79.27 -
Num. residues----580
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0024818
X-RAY DIFFRACTIONf_angle_d0.4256530
X-RAY DIFFRACTIONf_chiral_restr0.034724
X-RAY DIFFRACTIONf_plane_restr0.003786
X-RAY DIFFRACTIONf_dihedral_angle_d11.1282684
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A2463X-RAY DIFFRACTION7.343TORSIONAL
12B2463X-RAY DIFFRACTION7.343TORSIONAL
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 (%)
2.35-2.40870.44861340.40482328246298
2.4087-2.47380.37581430.378423482491100
2.4738-2.54660.36011390.342123472486100
2.5466-2.62870.34631430.329223582501100
2.6287-2.72260.32681350.297523332468100
2.7226-2.83150.29891500.27323482498100
2.8315-2.96030.29111390.258823632502100
2.9603-3.11610.30491420.263823542496100
3.1161-3.31110.26051470.258623672514100
3.3111-3.56640.2611380.235823822520100
3.5664-3.92450.25121410.23323742515100
3.9245-4.49050.23061430.221323972540100
4.4905-5.65060.25121460.212723862532100
5.6506-28.85220.22721480.22152462261099

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