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- PDB-8hbs: Crystal of rAlfNmt -

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Basic information

Entry
Database: PDB / ID: 8hbs
TitleCrystal of rAlfNmt
ComponentsGlycylpeptide N-tetradecanoyltransferase
KeywordsGENE REGULATION / Aspergillus flavus / N-myristoyltranferase
Function / homology
Function and homology information


N-terminal protein myristoylation / glycylpeptide N-tetradecanoyltransferase / glycylpeptide N-tetradecanoyltransferase activity / 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 / Acyl-CoA N-acyltransferase
Similarity search - Domain/homology
Glycylpeptide N-tetradecanoyltransferase
Similarity search - Component
Biological speciesAspergillus flavus (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.78 Å
AuthorsWang, Y. / Wang, S.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31972214 China
CitationJournal: Microbiol Spectr / Year: 2023
Title: N -Myristoyltransferase, a Potential Antifungal Candidate Drug-Target for Aspergillus flavus.
Authors: Wang, Y. / Lin, R. / Liu, M. / Wang, S. / Chen, H. / Zeng, W. / Nie, X. / Wang, S.
History
DepositionOct 30, 2022Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Mar 8, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 8, 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: Glycylpeptide N-tetradecanoyltransferase


Theoretical massNumber of molelcules
Total (without water)47,3231
Polymers47,3231
Non-polymers00
Water4,594255
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)97.823, 97.823, 47.116
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number76
Space group name H-MP41
Space group name HallP4w
Symmetry operation#1: x,y,z
#2: -y,x,z+1/4
#3: y,-x,z+3/4
#4: -x,-y,z+1/2

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Components

#1: Protein Glycylpeptide N-tetradecanoyltransferase


Mass: 47323.156 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aspergillus flavus (strain ATCC 200026 / FGSC A1120 / IAM 13836 / NRRL 3357 / JCM 12722 / SRRC 167) (mold)
Gene: AFLA_111720, G4B84_004850 / Production host: Escherichia coli (E. coli)
References: UniProt: B8N9M6, glycylpeptide N-tetradecanoyltransferase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 255 / 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: 2.38 Å3/Da / Density % sol: 48.36 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / Details: 0.1 M Tris, pH7.5, 20%(w/v) PEG 8000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.979 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Aug 30, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.78→43.75 Å / Num. obs: 42043 / % possible obs: 98.3 % / Redundancy: 2 % / Biso Wilson estimate: 29.68 Å2 / CC1/2: 0.999 / Net I/σ(I): 22.73
Reflection shellResolution: 1.78→1.847 Å / Num. unique obs: 3384 / CC1/2: 0.828

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
PROCORdata reduction
autoPROCdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4CAV

4cav


Resolution: 1.78→43.75 Å / SU ML: 0.2193 / Cross valid method: FREE R-VALUE / σ(F): 0.01 / Phase error: 26.0185
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2367 1957 4.74 %
Rwork0.2049 39333 -
obs0.2064 41290 96.4 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 35.6 Å2
Refinement stepCycle: LAST / Resolution: 1.78→43.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3210 0 0 255 3465
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00753298
X-RAY DIFFRACTIONf_angle_d1.06474475
X-RAY DIFFRACTIONf_chiral_restr0.0677489
X-RAY DIFFRACTIONf_plane_restr0.0117565
X-RAY DIFFRACTIONf_dihedral_angle_d6.0465430
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.78-1.830.38131150.29452235X-RAY DIFFRACTION77.76
1.83-1.880.32961220.27312514X-RAY DIFFRACTION86.63
1.88-1.930.30961390.2652697X-RAY DIFFRACTION93.47
1.93-1.990.26231430.25362797X-RAY DIFFRACTION97.09
1.99-2.070.28151420.24192850X-RAY DIFFRACTION98.36
2.07-2.150.25821450.23162890X-RAY DIFFRACTION98.96
2.15-2.250.31541380.23222864X-RAY DIFFRACTION99.21
2.25-2.360.24181410.24042869X-RAY DIFFRACTION99.05
2.36-2.510.2721400.24412921X-RAY DIFFRACTION99.71
2.51-2.710.26651410.23582902X-RAY DIFFRACTION99.71
2.71-2.980.25191480.22442904X-RAY DIFFRACTION99.9
2.98-3.410.26791440.20872943X-RAY DIFFRACTION100
3.41-4.290.20731470.17072946X-RAY DIFFRACTION99.94
4.3-43.750.17181520.16213001X-RAY DIFFRACTION99.43

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