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- PDB-6bms: Palmitoyltransferase structure -

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Basic information

Entry
Database: PDB / ID: 6bms
TitlePalmitoyltransferase structure
ComponentsPalmitoyltransferasePalmitoyl-CoA
KeywordsMEMBRANE 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
Palmitoyltransferase, DHHC domain / DHHC palmitoyltransferase / DHHC domain profile.
Similarity search - Domain/homology
PALMITIC ACID / PHOSPHATE ION / Chem-POV / Palmitoyltransferase ZDHHC15B
Similarity search - Component
Biological speciesDanio rerio (zebrafish)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.441 Å
AuthorsKumar, P. / Rajashankar, K.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/Eunice Kennedy Shriver National Institute of Child Health & Human Development (NIH/NICHD) United States
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 10, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2018Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.pdbx_database_id_DOI ..._citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Feb 28, 2018Group: Database references / Category: citation / Item: _citation.title
Revision 1.3Mar 28, 2018Group: Data collection / Database references / Category: citation / Item: _citation.title
Revision 1.4Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Mar 13, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Palmitoyltransferase
D: Palmitoyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,74017
Polymers79,3682
Non-polymers4,37315
Water86548
1
A: Palmitoyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,4589
Polymers39,6841
Non-polymers2,7748
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
D: Palmitoyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,2828
Polymers39,6841
Non-polymers1,5987
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)186.402, 186.402, 90.177
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number94
Space group name H-MP42212

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Components

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Protein / Sugars , 2 types, 7 molecules AD

#1: Protein Palmitoyltransferase / Palmitoyl-CoA


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 / DODECYL-BETA-D-MALTOSIDE


Type: D-saccharide / Mass: 510.615 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C24H46O11 / Comment: detergent*YM

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Non-polymers , 5 types, 58 molecules

#2: Chemical
ChemComp-ZN / ZINC ION


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


Mass: 256.424 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C16H32O2
#5: Chemical ChemComp-POV / (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate / POPC / POPC


Mass: 760.076 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C42H82NO8P / Comment: phospholipid*YM
#6: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: PO4
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 48 / 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: 5.1 Å3/Da / Density % sol: 75.99 % / Description: Diamond like
Crystal growTemperature: 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

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Data collection

DiffractionMean temperature: 97 K / Ambient temp details: 97
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 0.9797 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Jul 8, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9797 Å / Relative weight: 1
ReflectionResolution: 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 shellResolution: 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

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
HKL-2000data reduction
SCALEPACKdata scaling
RESOLVEphasing
RefinementMethod 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
RfactorNum. reflection% reflectionSelection details
Rfree0.2608 2974 5.05 %5%
Rwork0.2325 ---
obs0.2339 58857 99.14 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.441→37.213 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4584 0 231 48 4863
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0034964
X-RAY DIFFRACTIONf_angle_d0.5986721
X-RAY DIFFRACTIONf_dihedral_angle_d5.6782793
X-RAY DIFFRACTIONf_chiral_restr0.039739
X-RAY DIFFRACTIONf_plane_restr0.004795
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4413-2.48130.32461060.31222245X-RAY DIFFRACTION85
2.4813-2.5240.30031210.30592646X-RAY DIFFRACTION98
2.524-2.56990.32641380.29822635X-RAY DIFFRACTION100
2.5699-2.61930.28321460.28632633X-RAY DIFFRACTION100
2.6193-2.67280.30831480.27562638X-RAY DIFFRACTION100
2.6728-2.73090.28961580.26942659X-RAY DIFFRACTION100
2.7309-2.79440.28851390.25042625X-RAY DIFFRACTION100
2.7944-2.86430.28981300.25182669X-RAY DIFFRACTION100
2.8643-2.94170.26521460.24092643X-RAY DIFFRACTION100
2.9417-3.02820.25211240.22192701X-RAY DIFFRACTION100
3.0282-3.12590.25371660.22692636X-RAY DIFFRACTION100
3.1259-3.23760.28611500.23992656X-RAY DIFFRACTION100
3.2376-3.36710.26031510.23642661X-RAY DIFFRACTION100
3.3671-3.52020.24531520.23022671X-RAY DIFFRACTION100
3.5202-3.70570.23981350.21462687X-RAY DIFFRACTION100
3.7057-3.93760.25981430.21682695X-RAY DIFFRACTION100
3.9376-4.24120.25321500.20672695X-RAY DIFFRACTION100
4.2412-4.66730.23161360.20472713X-RAY DIFFRACTION100
4.6673-5.3410.21671600.20682735X-RAY DIFFRACTION100
5.341-6.72260.2251260.24742775X-RAY DIFFRACTION100
6.7226-37.2170.31021490.24862865X-RAY DIFFRACTION98
Refinement TLS params.Method: refined / Origin x: -47.0637 Å / Origin y: -1.4883 Å / Origin z: -24.89 Å
111213212223313233
T0.7399 Å2-0.0036 Å2-0.0663 Å2-0.3516 Å20.0029 Å2--0.5102 Å2
L-0.1403 °20.619 °20 °2-3.7147 °20.513 °2---0.1681 °2
S0.0635 Å °0.0146 Å °-0.0135 Å °0.3436 Å °-0.0859 Å °-0.0157 Å °-0.0249 Å °-0.0161 Å °0.0231 Å °
Refinement TLS groupSelection details: all

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