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- PDB-6omk: Crystal structure of a glycylpeptide N-tetradecanoyltransferase (... -

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Basic information

Entry
Database: PDB / ID: 6omk
TitleCrystal structure of a glycylpeptide N-tetradecanoyltransferase (N-myristoyl transferase, NMT) from Leishmania major Friedlin bound to tetradecanoyl-CoA
ComponentsGlycylpeptide N-tetradecanoyltransferase
KeywordsTRANSFERASE / NIAID / structural genomics / SVTD / SDDC / NMT1 / myristic acid / Seattle Structural Genomics Center for Infectious Disease / SSGCID
Function / homology
Function and homology information


N-terminal protein myristoylation / glycylpeptide N-tetradecanoyltransferase / glycylpeptide N-tetradecanoyltransferase activity
Similarity search - Function
Aminopeptidase - #170 / Glycylpeptide N-tetradecanoyltransferase, conserved site / Myristoyl-CoA:protein N-myristoyltransferase signature 1. / Myristoyl-CoA:protein N-myristoyltransferase signature 2. / Glycylpeptide N-tetradecanoyltransferase / Glycylpeptide N-tetradecanoyltransferase, N-terminal / Glycylpeptide N-tetradecanoyltransferase, C-terminal / Myristoyl-CoA:protein N-myristoyltransferase, N-terminal domain / Myristoyl-CoA:protein N-myristoyltransferase, C-terminal domain / Acyl-CoA N-acyltransferase ...Aminopeptidase - #170 / Glycylpeptide N-tetradecanoyltransferase, conserved site / Myristoyl-CoA:protein N-myristoyltransferase signature 1. / Myristoyl-CoA:protein N-myristoyltransferase signature 2. / Glycylpeptide N-tetradecanoyltransferase / Glycylpeptide N-tetradecanoyltransferase, N-terminal / Glycylpeptide N-tetradecanoyltransferase, C-terminal / Myristoyl-CoA:protein N-myristoyltransferase, N-terminal domain / Myristoyl-CoA:protein N-myristoyltransferase, C-terminal domain / Acyl-CoA N-acyltransferase / Aminopeptidase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
TETRADECANOYL-COA / Glycylpeptide N-tetradecanoyltransferase
Similarity search - Component
Biological speciesLeishmania major (eukaryote)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.1 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: To Be Published
Title: Crystal structure of a glycylpeptide N-tetradecanoyltransferase (N-myristoyl transferase, NMT) from Leishmania major Friedlin bound to tetradecanoyl-CoA
Authors: Edwards, T.E. / Horanyi, P.S. / Bertolin, B.A. / Lorimer, D.D. / Seattle Structural Genomics Center for Infectious Disease (SSGCID)
History
DepositionApr 18, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 1, 2019Provider: repository / Type: Initial release
Revision 1.1Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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: Glycylpeptide N-tetradecanoyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,2556
Polymers49,0261
Non-polymers1,2305
Water3,945219
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)49.250, 89.170, 90.360
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Glycylpeptide N-tetradecanoyltransferase


Mass: 49025.785 Da / Num. of mol.: 1 / Fragment: residues 6-421
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Leishmania major (eukaryote) / Strain: Friedlin / Gene: NMT / Production host: Escherichia coli (E. coli)
References: UniProt: Q9GPZ4, glycylpeptide N-tetradecanoyltransferase
#2: Chemical ChemComp-MYA / TETRADECANOYL-COA / MYRISTOYL-COA


Mass: 977.890 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C35H62N7O17P3S
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 219 / 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: 2.02 Å3/Da / Density % sol: 39.22 %
Crystal growTemperature: 287 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: LemaA.18219.a.B1.PS38467 at 3.52 mg/mL with 0.5 mM myristoyl CoA (tetradecanoyl CoA) against 16% PEG 3350, 0.2 M NaCl, 0.1 M sodium cacodylate pH 5.6, supplemented with 20% ethylene glycol ...Details: LemaA.18219.a.B1.PS38467 at 3.52 mg/mL with 0.5 mM myristoyl CoA (tetradecanoyl CoA) against 16% PEG 3350, 0.2 M NaCl, 0.1 M sodium cacodylate pH 5.6, supplemented with 20% ethylene glycol as cryo-protectant, crystal tracking ID 303026d4, unique puck ID vle8-4

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.5406 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: Aug 29, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5406 Å / Relative weight: 1
ReflectionResolution: 2.1→44.585 Å / Num. obs: 23914 / % possible obs: 100 % / Redundancy: 6.875 % / Biso Wilson estimate: 33.365 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.103 / Rrim(I) all: 0.112 / Χ2: 0.943 / Net I/σ(I): 12.54 / Num. measured all: 164416 / Scaling rejects: 10
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
2.1-2.156.0320.5523.510592175617560.8740.605100
2.15-2.216.9390.4524.7311692168516850.9280.489100
2.21-2.286.7630.424.9911071163916370.9330.45599.9
2.28-2.356.9630.3585.5411322162616260.9480.387100
2.35-2.427.0440.316.410777153015300.9630.334100
2.42-2.517.020.2717.0510664152015190.9740.29399.9
2.51-2.67.0620.2387.8710289145714570.9810.257100
2.6-2.716.9970.2049.319810140214020.9810.221100
2.71-2.837.0560.16110.739540135213520.9890.174100
2.83-2.977.0750.1312.649162129512950.9930.141100
2.97-3.137.0310.10814.68627122712270.9950.117100
3.13-3.3270.0916.858309118711870.9950.097100
3.32-3.556.8280.07719.947497109910980.9960.08399.9
3.55-3.836.8110.06623.686988102710260.9970.07199.9
3.83-4.26.9010.05825.5165499499490.9970.063100
4.2-4.76.9270.05727.9261038818810.9970.062100
4.7-5.427.0150.05726.6254587787780.9970.062100
5.42-6.646.9060.06623.5545726626620.9960.072100
6.64-9.396.6570.05926.7635485335330.9970.064100
9.39-44.5855.8790.05828.9718463193140.9960.06398.4

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
PHENIX(1.15_3459)refinement
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3H5Z

3h5z


Resolution: 2.1→44.585 Å / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 22.53
RfactorNum. reflection% reflection
Rfree0.2327 2000 8.36 %
Rwork0.1696 --
obs0.1748 23914 99.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 98.59 Å2 / Biso mean: 32.0067 Å2 / Biso min: 11.8 Å2
Refinement stepCycle: final / Resolution: 2.1→44.585 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3352 0 76 220 3648
Biso mean--25.34 38.66 -
Num. residues----417
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.0999-2.15250.30991340.212215551689
2.1525-2.21070.24461070.183915541661
2.2107-2.27570.27531460.188915321678
2.2757-2.34920.27381440.18715551699
2.3492-2.43310.24781370.18515481685
2.4331-2.53050.29091360.184115331669
2.5305-2.64570.24351530.179615361689
2.6457-2.78510.22831260.171215761702
2.7851-2.95960.23171480.169915381686
2.9596-3.18810.21451550.163915651720
3.1881-3.50880.21021420.156815741716
3.5088-4.01620.22471450.149115751720
4.0162-5.05890.19721440.148816111755
5.0589-44.5950.24261830.191716621845
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.17120.02960.14143.59920.43882.56080.09810.30010.0602-0.1879-0.05480.0019-0.05060.03-0.04570.1440.01610.02080.22460.01560.135724.2282-10.4795-14.5209
23.23610.5704-3.1072.00991.32516.40240.07370.10860.1894-0.2447-0.0520.0861-0.2758-0.2855-0.0240.23090.0506-0.00450.12630.02020.155414.51093.894-1.7083
30.93010.039-0.06421.57090.3791.65450.0508-0.00910.0521-0.0368-0.04420.1165-0.1294-0.0555-0.00870.1438-0.0140.02140.1673-0.02350.172416.4656-2.780510.2077
42.0725-0.5015-0.24561.968-0.81360.45040.07950.3057-0.2151-0.6161-0.1180.21270.04-0.10660.15190.22790.0074-0.06520.27010.01760.205813.8549-15.955-15.2487
51.7405-0.005-0.00242.00670.24211.8230.05430.23640.1547-0.331-0.0342-0.3664-0.08760.3376-0.04250.1968-0.00830.07930.26720.02680.219332.9791-5.5593-10.2025
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 333 through 397 )A333 - 397
2X-RAY DIFFRACTION2chain 'A' and (resid 398 through 421 )A398 - 421
3X-RAY DIFFRACTION3chain 'A' and (resid -1 through 204 )A-1 - 204
4X-RAY DIFFRACTION4chain 'A' and (resid 205 through 244 )A205 - 244
5X-RAY DIFFRACTION5chain 'A' and (resid 245 through 332 )A245 - 332

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