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- PDB-1nmt: N-MYRISTOYL TRANSFERASE FROM CANDIDA ALBICANS AT 2.45 A -

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Basic information

Entry
Database: PDB / ID: 1nmt
TitleN-MYRISTOYL TRANSFERASE FROM CANDIDA ALBICANS AT 2.45 A
ComponentsN-MYRISTOYL TRANSFERASE
KeywordsMYRISTYLATION / ANTIFUNGAL TARGET / COA / TRANSFERASE / ACYLTRANSFERASE
Function / homology
Function and homology information


glycylpeptide N-tetradecanoyltransferase / glycylpeptide N-tetradecanoyltransferase activity / cytoplasm / cytosol
Similarity search - Function
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 / Gcn5-related N-acetyltransferase (GNAT) / Acyl-CoA N-acyltransferase ...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 / Gcn5-related N-acetyltransferase (GNAT) / Acyl-CoA N-acyltransferase / Aminopeptidase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Glycylpeptide N-tetradecanoyltransferase
Similarity search - Component
Biological speciesCandida albicans (yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIR / Resolution: 2.45 Å
AuthorsWeston, S.A. / Pauptit, R.A.
Citation
#1: Journal: To be Published
Title: Refinement of N-Myryistoyl Transferase at 2.45A
Authors: Rowsell, S. / Pauptit, R.A.
History
DepositionDec 11, 1997Processing site: BNL
Revision 1.0Jan 13, 1999Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: N-MYRISTOYL TRANSFERASE
B: N-MYRISTOYL TRANSFERASE
C: N-MYRISTOYL TRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)137,92221
Polymers136,2653
Non-polymers1,65818
Water5,242291
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)132.000, 166.500, 179.400
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(0.309521, 0.948404, 0.068751), (-0.933647, 0.31682, -0.167118), (-0.180277, -0.012463, 0.983537)-7.60747, 37.2413, 25.62448
2given(-0.678004, 0.698721, -0.228253), (-0.696603, -0.709893, -0.103908), (-0.234639, 0.088552, 0.968041)16.3797, 54.07578, 39.26222

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Components

#1: Protein N-MYRISTOYL TRANSFERASE


Mass: 45421.566 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Candida albicans (yeast) / Cellular location: CYTOPLASM / Production host: Escherichia coli (E. coli)
References: UniProt: P30418, glycylpeptide N-tetradecanoyltransferase
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 18 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 291 / Source method: isolated from a natural source / Formula: H2O
Compound detailsAPOENZYME STRUCTURE. ENZYME BINDS MYRISTYL COA (PRESUMABLY IN GROOVE) PLUS SUBSTRATE PROTEIN N- ...APOENZYME STRUCTURE. ENZYME BINDS MYRISTYL COA (PRESUMABLY IN GROOVE) PLUS SUBSTRATE PROTEIN N-TERMINUS (IN DEEP POCKET). TERMINAL LEU: BURIED AT FLOOR OF CATALYTIC POCKET

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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: 3.8 Å3/Da / Density % sol: 68 %
Crystal growpH: 7 / Details: pH 7.0
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
110 mg/mlprotein1drop
2100 mMTris-HCl1drop
31 mMdithiothreitol1drop
41 mMEDTA1drop
5100 mMTris-HCl1reservoir
610 %(w/v)PEG40001reservoir
715 %(v/v)glycerol1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX9.6 / Wavelength: 0.87
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: May 18, 1995 / Details: VERTICALLY-FOCUSED PT-COATED MIRROR
RadiationMonochromator: SI(111) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.87 Å / Relative weight: 1
ReflectionResolution: 2.45→20.85 Å / Num. obs: 72615 / % possible obs: 98.6 % / Observed criterion σ(I): 0 / Redundancy: 4.1 % / Biso Wilson estimate: 32.2 Å2 / Rmerge(I) obs: 0.047 / Rsym value: 0.047 / Net I/σ(I): 13.9
Reflection shellResolution: 2.45→2.58 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.318 / Mean I/σ(I) obs: 2.4 / Rsym value: 0.318 / % possible all: 95.5
Reflection shell
*PLUS
% possible obs: 95.5 %

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Processing

Software
NameVersionClassification
SHARPphasing
X-PLOR3.98refinement
MOSFLMdata reduction
CCP4data scaling
RefinementMethod to determine structure: SIR / Resolution: 2.45→20.85 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 1000000 / Data cutoff low absF: 0.001 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2
Details: BULK SOLVENT MODEL USED. 18 GLYCEROL MOLECULES INCLUDED AS FRA 1 - 18.
RfactorNum. reflection% reflectionSelection details
Rfree0.251 3703 5.1 %RANDOM
Rwork0.214 ---
obs0.214 72615 98.3 %-
Displacement parametersBiso mean: 38.4 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.36 Å0.3 Å
Luzzati d res low-5 Å
Luzzati sigma a0.41 Å0.32 Å
Refinement stepCycle: LAST / Resolution: 2.45→20.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9602 0 108 291 10001
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.011
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.6
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d26.6
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d0.82
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it3.652
X-RAY DIFFRACTIONx_mcangle_it4.972.5
X-RAY DIFFRACTIONx_scbond_it5.952.5
X-RAY DIFFRACTIONx_scangle_it7.273
Refine LS restraints NCSNCS model details: RESTRAIN / Rms dev Biso : 7.26 Å2 / Weight Biso : 3 / Weight position: 100
LS refinement shellResolution: 2.45→2.6 Å / Rfactor Rfree error: 0.016 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.372 564 4.8 %
Rwork0.315 11073 -
obs--95.3 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMTOPHCSDX.PRO
X-RAY DIFFRACTION2FRA.PARTOPH19.SOL
X-RAY DIFFRACTION3FRA.TOP
Software
*PLUS
Name: X-PLOR / Version: 98 / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg26.6
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg0.82
LS refinement shell
*PLUS
Rfactor obs: 0.315

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