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- PDB-1kp9: Crystal structure of mycolic acid cyclopropane synthase CmaA1, ap... -

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Basic information

Entry
Database: PDB / ID: 1kp9
TitleCrystal structure of mycolic acid cyclopropane synthase CmaA1, apo-form
ComponentsCYCLOPROPANE-FATTY-ACYL-PHOSPHOLIPID SYNTHASE 1
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 / S-adenosylmethionine metabolic process / mycolic acid biosynthetic process / lipid biosynthetic process / methylation / plasma membrane / 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
ACETIC ACID / Cyclopropane mycolic acid synthase 1 / Cyclopropane mycolic acid synthase 1
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.21 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: 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: CYCLOPROPANE-FATTY-ACYL-PHOSPHOLIPID SYNTHASE 1
B: CYCLOPROPANE-FATTY-ACYL-PHOSPHOLIPID SYNTHASE 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,1755
Polymers64,9942
Non-polymers1803
Water3,477193
1
A: CYCLOPROPANE-FATTY-ACYL-PHOSPHOLIPID SYNTHASE 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,5572
Polymers32,4971
Non-polymers601
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: CYCLOPROPANE-FATTY-ACYL-PHOSPHOLIPID SYNTHASE 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,6173
Polymers32,4971
Non-polymers1202
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)50.342, 73.812, 76.043
Angle α, β, γ (deg.)90.00, 107.07, 90.00
Int Tables number4
Cell settingmonoclinic
Space group name H-MP1211

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Components

#1: Protein CYCLOPROPANE-FATTY-ACYL-PHOSPHOLIPID SYNTHASE 1 / E.C.2.1.1.79 / CYCLOPROPANE FATTY ACID SYNTHASE / CFA SYNTHASE / CYCLOPROPANE MYCOLIC ACID SYNTHASE / cmaA1


Mass: 32497.176 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: cmaA1 / Plasmid: pET30b(cmaA1) / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: Q11195, UniProt: P9WPB7*PLUS, cyclopropane-fatty-acyl-phospholipid synthase
#2: Chemical ChemComp-ACY / ACETIC ACID


Mass: 60.052 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H4O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 193 / 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: 2.08 Å3/Da / Density % sol: 40.81 %
Crystal growTemperature: 292 K / Method: evaporation / pH: 6.5
Details: PEG 4000, sodium acetate, MES , ammonium acetate, 1,6-hexadiol, pH 6.5, EVAPORATION at 292K
Crystal grow
*PLUS
Temperature: 19 ℃ / Method: batch method
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
17-10 mg/mlprotein11
222 %PEG400011
30.2 MMES11pH6.5
40.3 M11CH3CO2NH4
53 %1,6-hexanediol11

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: MACSCIENCE / Detector: IMAGE PLATE / Date: Feb 15, 2001 / Details: osmic mirrors
RadiationMonochromator: Ni FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.2→30 Å / Num. all: 23312 / Num. obs: 23312 / % possible obs: 87.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 1.94 % / Biso Wilson estimate: 20.8 Å2 / Rsym value: 0.062 / Net I/σ(I): 17.2
Reflection shellResolution: 2.2→2.34 Å / Mean I/σ(I) obs: 4.3 / Rsym value: 0.183 / % possible all: 73.2
Reflection
*PLUS
Lowest resolution: 30 Å / Num. measured all: 45181 / Rmerge(I) obs: 0.062
Reflection shell
*PLUS
% possible obs: 73.2 % / Rmerge(I) obs: 0.183

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNS1.1refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.21→29.29 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 330464.75 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: CNS
RfactorNum. reflection% reflectionSelection details
Rfree0.254 2184 9.8 %RANDOM
Rwork0.2 ---
obs0.2 22287 83 %-
all-23312 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 29.267 Å2 / ksol: 0.295527 e/Å3
Displacement parametersBiso mean: 36.1 Å2
Baniso -1Baniso -2Baniso -3
1--0.62 Å20 Å27.77 Å2
2---0.51 Å20 Å2
3---1.13 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.33 Å0.25 Å
Luzzati d res low-5 Å
Luzzati sigma a0.32 Å0.23 Å
Refinement stepCycle: LAST / Resolution: 2.21→29.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4288 0 0 205 4493
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_d22.2
X-RAY DIFFRACTIONc_improper_angle_d0.72
X-RAY DIFFRACTIONc_mcbond_it1.451.5
X-RAY DIFFRACTIONc_mcangle_it2.392
X-RAY DIFFRACTIONc_scbond_it2.042
X-RAY DIFFRACTIONc_scangle_it2.922.5
LS refinement shellResolution: 2.2→2.34 Å / Rfactor Rfree error: 0.02 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.304 241 9.1 %
Rwork0.242 2404 -
obs--59.1 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3OAC.PAROAC.TOP
Software
*PLUS
Name: CNS / Version: 1.1 / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.2 Å / Lowest resolution: 30 Å / σ(F): 2 / % reflection Rfree: 10 % / Rfactor obs: 0.2 / Rfactor Rwork: 0.2
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 36.1 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.0067
X-RAY DIFFRACTIONc_angle_deg1.27
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg22.2
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.72
X-RAY DIFFRACTIONc_mcbond_it1.451.5
X-RAY DIFFRACTIONc_scbond_it2.042
X-RAY DIFFRACTIONc_mcangle_it2.392
X-RAY DIFFRACTIONc_scangle_it2.922.5
LS refinement shell
*PLUS
Rfactor Rfree: 0.304 / % reflection Rfree: 9.1 % / Rfactor Rwork: 0.242

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