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- PDB-1l1e: Crystal Structure of Mycolic Acid Cyclopropane Synthase PcaA Comp... -

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Basic information

Entry
Database: PDB / ID: 1l1e
TitleCrystal Structure of Mycolic Acid Cyclopropane Synthase PcaA Complexed with S-adenosyl-L-homocysteine
Componentsmycolic acid synthase
KeywordsTRANSFERASE / METHYLTRANSFERASE / S-ADENOSYL-L-HOMOCYSTEINE COFACTOR / ALPHA/BETA / Structural Genomics / PSI / Protein Structure Initiative / TB Structural Genomics Consortium / TBSGC
Function / homology
Function and homology information


cyclopropane-fatty-acyl-phospholipid synthase / cyclopropane-fatty-acyl-phospholipid synthase activity / symbiont-mediated perturbation of host innate immune response / S-adenosylmethionine metabolic process / mycolic acid biosynthetic process / evasion of host immune response / lipid biosynthetic process / : / methylation / cytoplasm
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
CARBONATE ION / S-ADENOSYL-L-HOMOCYSTEINE / Cyclopropane mycolic acid synthase 3 / Cyclopropane mycolic acid synthase 3
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2 Å
AuthorsHuang, C.-C. / Smith, C.V. / Glickman, M.S. / Jacobs Jr., W.R. / Sacchettini, J.C. / TB Structural Genomics Consortium (TBSGC)
CitationJournal: J.Biol.Chem. / Year: 2002
Title: Crystal structures of mycolic acid cyclopropane synthases from Mycobacterium tuberculosis.
Authors: Huang, C.-C. / Smith, C.V. / Glickman, M.S. / Jacobs Jr., W.R. / Sacchettini, J.C.
History
DepositionFeb 15, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 6, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: 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: mycolic acid synthase
B: mycolic acid synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,0306
Polymers66,1412
Non-polymers8894
Water3,603200
1
A: mycolic acid synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,5153
Polymers33,0711
Non-polymers4442
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: mycolic acid synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,5153
Polymers33,0711
Non-polymers4442
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)45.340, 45.340, 446.020
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65
DetailsBiological assembly is a monomer

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Components

#1: Protein mycolic acid synthase / PcaA cyclopropane synthase


Mass: 33070.676 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: pcaA / Plasmid: pET30b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: Q7D9R5, UniProt: P9WPB3*PLUS, cyclopropane-fatty-acyl-phospholipid synthase
#2: Chemical ChemComp-CO3 / CARBONATE ION / Carbonate


Mass: 60.009 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CO3
#3: Chemical ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE / S-Adenosyl-L-homocysteine


Type: L-peptide linking / Mass: 384.411 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H20N6O5S
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 200 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2 Å3/Da / Density % sol: 38.53 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 4.8
Details: PEG 6000, sodium acetate, n-octanoylsucrose, S-adenosyl-L-homocysteine, pH 4.8, VAPOR DIFFUSION, HANGING DROP, temperature 292K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONAPS 14-BM-C11
SYNCHROTRONAPS 14-BM-D20.9793, 0.9795, 0.9641
Detector
TypeIDDetectorDateDetails
ADSC QUANTUM 41CCDAug 20, 2000bent conical Si-mirror (Rh coating) bend cylindrical Ge(111) monochromator
ADSC QUANTUM 42CCDMar 10, 2000bent cylindrical Si-mirror (Rh coating) Si(111) double-crystal monochromato
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1bend cylindrical Ge(111) monochromatorSINGLE WAVELENGTHMx-ray1
2Si(111) double-crystal monochromatorMADMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
111
20.97931
30.97951
40.96411
ReflectionResolution: 2→30 Å / Num. all: 33417 / Num. obs: 33305 / % possible obs: 98 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 3 / Biso Wilson estimate: 19.3 Å2
Reflection shellResolution: 2→2.07 Å / % possible all: 93.4

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
SHARPphasing
CNS1refinement
RefinementMethod to determine structure: MAD / Resolution: 2→28.21 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 450578.69 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 3 / Stereochemistry target values: Engh & Huber
Details: The electron density in the region of A175 to A180 was weak. The main chain was built in; however, there is some difficulty in fitting the side chain of Glu176, leading to a close contact ...Details: The electron density in the region of A175 to A180 was weak. The main chain was built in; however, there is some difficulty in fitting the side chain of Glu176, leading to a close contact with Lys180. The electron density corresponding to residues B176-B187 was not present. These residues were not built into the model.
RfactorNum. reflection% reflectionSelection details
Rfree0.27 1619 5 %RANDOM
Rwork0.222 ---
all0.235 33417 --
obs0.222 32625 95.7 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 37.1262 Å2 / ksol: 0.288251 e/Å3
Displacement parametersBiso mean: 33.9 Å2
Baniso -1Baniso -2Baniso -3
1-2 Å21.83 Å20 Å2
2--2 Å20 Å2
3----4.01 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.31 Å0.24 Å
Luzzati d res low-5 Å
Luzzati sigma a0.24 Å0.14 Å
Refinement stepCycle: LAST / Resolution: 2→28.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4331 0 60 200 4591
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d21.8
X-RAY DIFFRACTIONc_improper_angle_d0.84
X-RAY DIFFRACTIONc_mcbond_it1.51.5
X-RAY DIFFRACTIONc_mcangle_it2.32
X-RAY DIFFRACTIONc_scbond_it2.062
X-RAY DIFFRACTIONc_scangle_it2.892.5
LS refinement shellResolution: 2→2.13 Å / Rfactor Rfree error: 0.021 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.296 204 4.9 %
Rwork0.231 3932 -
obs--71.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3SAH.PARAMSAH.TOP
X-RAY DIFFRACTION4ION.PARAMION.TOP

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