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- PDB-1tpy: Structure of the cyclopropane synthase MmaA2 from Mycobacterium t... -

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Basic information

Entry
Database: PDB / ID: 1tpy
TitleStructure of the cyclopropane synthase MmaA2 from Mycobacterium tuberculosis
Componentsmethoxy mycolic acid synthase 2
KeywordsTRANSFERASE / Methyltransferase / cyclopropane synthase / mycolic acids / tuberculosis / SAM-dependent
Function / homology
Function and homology information


cyclopropane-fatty-acyl-phospholipid synthase / cyclopropane-fatty-acyl-phospholipid synthase activity / mycolic acid biosynthetic process / lipid biosynthetic process / peptidoglycan-based cell wall / methyltransferase activity / methylation / plasma membrane
Similarity search - Function
: / Mycolic acid cyclopropane synthase / : / Mycolic acid cyclopropane synthetase / Vaccinia Virus protein VP39 / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
CETYL-TRIMETHYL-AMMONIUM / CARBONATE ION / S-ADENOSYL-L-HOMOCYSTEINE / Cyclopropane mycolic acid synthase MmaA2
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsSmith, C.V. / Sacchettini, J.C.
CitationJournal: To be Published
Title: Structure of the cyclopropane synthase MmaA2 from Mycobacterium tuberculosis
Authors: Smith, C.V. / Sacchettini, J.C.
History
DepositionJun 16, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 19, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 23, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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

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Assembly

Deposited unit
A: methoxy mycolic acid synthase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,4934
Polymers32,7641
Non-polymers7293
Water3,459192
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)42.587, 58.420, 133.683
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein methoxy mycolic acid synthase 2


Mass: 32764.281 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: mmaA2 / Plasmid: pET30b-mmaA2 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: Q79FX6, cyclopropane-fatty-acyl-phospholipid synthase
#2: Chemical ChemComp-CO3 / CARBONATE ION


Mass: 60.009 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CO3
#3: Chemical ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE


Type: L-peptide linking / Mass: 384.411 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H20N6O5S
#4: Chemical ChemComp-16A / CETYL-TRIMETHYL-AMMONIUM


Mass: 284.543 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H42N
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 192 / 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: 2.541 Å3/Da / Density % sol: 49.73 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: PEG 6000, MES buffer, cetyl trimethyl ammonium bromide, S-adenosyl-l-homocysteine, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 292K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.3 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Nov 15, 2002
RadiationMonochromator: Single crystal, cylindrically bent, Si(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. all: 17966 / Num. obs: 17358 / % possible obs: 96.6 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 3 / Redundancy: 3.9 % / Rmerge(I) obs: 0.0582 / Rsym value: 0.036 / Net I/σ(I): 10.8
Reflection shellResolution: 2.19→2.3 Å / % possible all: 84.9

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Processing

Software
NameClassification
HKL-2000data collection
SCALEPACKdata scaling
AMoREphasing
CNSrefinement
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PcaA ENTRY 1LIE

1lie


Resolution: 2.2→50 Å / Cross valid method: THROUGHOUT / σ(F): 3 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.232 1654 -RANDOM
Rwork0.194 ---
all0.244 17625 --
obs0.198 16498 93.6 %-
Displacement parametersBiso mean: 28.7 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.29 Å0.24 Å
Luzzati d res low-5 Å
Luzzati sigma a0.22 Å0.13 Å
Refinement stepCycle: LAST / Resolution: 2.2→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2292 0 50 192 2534
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_d1.3
X-RAY DIFFRACTIONc_dihedral_angle_d21.4
X-RAY DIFFRACTIONc_improper_angle_d0.78
X-RAY DIFFRACTIONc_mcbond_it1.22
X-RAY DIFFRACTIONc_mcangle_it1.84
LS refinement shellResolution: 2.2→2.34 Å / Rfactor Rfree error: 0.016
RfactorNum. reflection% reflection
Rfree0.243 227 -
Rwork0.205 --
obs-2154 82.1 %

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