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- PDB-1kpi: Crystal Structure of mycolic acid cyclopropane synthase CmaA2 com... -

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Basic information

Entry
Database: PDB / ID: 1kpi
TitleCrystal Structure of mycolic acid cyclopropane synthase CmaA2 complexed with SAH and DDDMAB
ComponentsCYCLOPROPANE-FATTY-ACYL-PHOSPHOLIPID SYNTHASE 2
KeywordsTRANSFERASE / mixed alpha beta fold / 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 / Actinobacterium-type cell wall biogenesis / symbiont-mediated perturbation of host innate immune response / mycolate cell wall layer assembly / S-adenosylmethionine metabolic process / mycolic acid biosynthetic process / lipid biosynthetic process / methylation / response to hypoxia ...cyclopropane-fatty-acyl-phospholipid synthase / cyclopropane-fatty-acyl-phospholipid synthase activity / Actinobacterium-type cell wall biogenesis / symbiont-mediated perturbation of host innate immune response / mycolate cell wall layer assembly / S-adenosylmethionine metabolic process / mycolic acid biosynthetic process / lipid biosynthetic process / methylation / response to hypoxia / plasma membrane / cytosol / 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
DIDECYL-DIMETHYL-AMMONIUM / CARBONATE ION / S-ADENOSYL-L-HOMOCYSTEINE / Cyclopropane mycolic acid synthase 2 / Cyclopropane mycolic acid synthase 2
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.65 Å
AuthorsHuang, C.-C. / Smith, C.V. / Jacobs Jr., W.R. / Glickman, M.S. / 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
DepositionDec 30, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 11, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / 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_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: CYCLOPROPANE-FATTY-ACYL-PHOSPHOLIPID SYNTHASE 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,7978
Polymers34,6421
Non-polymers1,1557
Water1,11762
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: CYCLOPROPANE-FATTY-ACYL-PHOSPHOLIPID SYNTHASE 2
hetero molecules

A: CYCLOPROPANE-FATTY-ACYL-PHOSPHOLIPID SYNTHASE 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,59516
Polymers69,2842
Non-polymers2,31114
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555x,-y+1/2,-z+1/41
Buried area5550 Å2
ΔGint-111 kcal/mol
Surface area22860 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)106.710, 106.710, 227.498
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number98
Cell settingtetragonal
Space group name H-MI4122

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Components

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Protein , 1 types, 1 molecules A

#1: Protein CYCLOPROPANE-FATTY-ACYL-PHOSPHOLIPID SYNTHASE 2 / / E.C.2.1.1.79 / CYCLOPROPANE FATTY ACID SYNTHASE / CFA SYNTHASE / CYCLOPROPANE MYCOLIC ACID SYNTHASE / cmaA2


Mass: 34642.023 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: cmaA2 / Plasmid: pET30b(cmaA1) / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: P0A5P0, UniProt: P9WPB5*PLUS, cyclopropane-fatty-acyl-phospholipid synthase

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Non-polymers , 5 types, 69 molecules

#2: Chemical ChemComp-CO3 / CARBONATE ION / Carbonate


Mass: 60.009 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CO3
#3: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE / S-Adenosyl-L-homocysteine


Type: L-peptide linking / Mass: 384.411 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H20N6O5S
#5: Chemical ChemComp-10A / DIDECYL-DIMETHYL-AMMONIUM


Mass: 326.623 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C22H48N
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 62 / 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: 4.67 Å3/Da / Density % sol: 73.68 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: ammonium sulfate, TRIS, SAH, DDDMAB, pH 8.5, VAPOR DIFFUSION, HANGING DROP at 292K
Crystal grow
*PLUS
Temperature: 19 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
10.5-2 mMSAH1drop
20.100-0.200 mMDDDMAB1drop
37-10 mg/mlprotein1drop
41.8 Mammonium sulfate1reservoir
50.1 MTris-HCl1reservoirpH8.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-BM-C / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 10, 2001 / Details: bent conical Si-mirror (Rh coating)
RadiationMonochromator: bend cylindrical Ge(111) monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.65→30 Å / Num. all: 21781 / Num. obs: 21781 / % possible obs: 96.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.3 % / Biso Wilson estimate: 46 Å2 / Rsym value: 0.062 / Net I/σ(I): 16.2
Reflection shellResolution: 2.65→2.82 Å / Mean I/σ(I) obs: 3.8 / Rsym value: 0.24 / % possible all: 78.3
Reflection
*PLUS
Highest resolution: 2.5 Å / Lowest resolution: 30 Å / Num. measured all: 94665 / Rmerge(I) obs: 0.062
Reflection shell
*PLUS
% possible obs: 78.3 % / Rmerge(I) obs: 0.24

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNS1.1refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.65→29.35 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 224483.38 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: CNS
RfactorNum. reflection% reflectionSelection details
Rfree0.242 1851 9.9 %RANDOM
Rwork0.208 ---
all0.208 18755 --
obs0.208 18755 96 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 38.1473 Å2 / ksol: 0.362734 e/Å3
Displacement parametersBiso mean: 43.6 Å2
Baniso -1Baniso -2Baniso -3
1--1.26 Å20 Å20 Å2
2---1.26 Å20 Å2
3---2.52 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.38 Å0.32 Å
Luzzati d res low-5 Å
Luzzati sigma a0.47 Å0.41 Å
Refinement stepCycle: LAST / Resolution: 2.65→29.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2363 0 73 62 2498
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_d21.7
X-RAY DIFFRACTIONc_improper_angle_d0.79
X-RAY DIFFRACTIONc_mcbond_it1.221.5
X-RAY DIFFRACTIONc_mcangle_it2.072
X-RAY DIFFRACTIONc_scbond_it1.892
X-RAY DIFFRACTIONc_scangle_it2.882.5
LS refinement shellResolution: 2.65→2.82 Å / Rfactor Rfree error: 0.018 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.317 295 10.2 %
Rwork0.287 2584 -
obs--90.3 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3ION.PARION.TOP
X-RAY DIFFRACTION4SAH.PARSAH.TOP
X-RAY DIFFRACTION5LIP.PARLIP.TOP
Software
*PLUS
Name: CNS / Version: 1.1 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 30 Å / σ(F): 2 / % reflection Rfree: 9.9 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 43.6 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.32
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg21.7
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.79
X-RAY DIFFRACTIONc_mcbond_it1.221.5
X-RAY DIFFRACTIONc_scbond_it1.892
X-RAY DIFFRACTIONc_mcangle_it2.072
X-RAY DIFFRACTIONc_scangle_it2.882.5
LS refinement shell
*PLUS
Rfactor Rfree: 0.317 / % reflection Rfree: 10.2 % / Rfactor Rwork: 0.287

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