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- PDB-1kph: Crystal Structure of mycolic acid cyclopropane synthase CmaA1 com... -

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Basic information

Entry
Database: PDB / ID: 1kph
TitleCrystal Structure of mycolic acid cyclopropane synthase CmaA1 complexed with SAH and DDDMAB
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
DIDECYL-DIMETHYL-AMMONIUM / CARBONATE ION / S-ADENOSYL-L-HOMOCYSTEINE / Cyclopropane mycolic acid synthase 1 / Cyclopropane mycolic acid synthase 1
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2 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
C: CYCLOPROPANE-FATTY-ACYL-PHOSPHOLIPID SYNTHASE 1
D: CYCLOPROPANE-FATTY-ACYL-PHOSPHOLIPID SYNTHASE 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)133,07316
Polymers129,9894
Non-polymers3,08412
Water13,187732
1
A: CYCLOPROPANE-FATTY-ACYL-PHOSPHOLIPID SYNTHASE 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,2684
Polymers32,4971
Non-polymers7713
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)33,2684
Polymers32,4971
Non-polymers7713
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: CYCLOPROPANE-FATTY-ACYL-PHOSPHOLIPID SYNTHASE 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,2684
Polymers32,4971
Non-polymers7713
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: CYCLOPROPANE-FATTY-ACYL-PHOSPHOLIPID SYNTHASE 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,2684
Polymers32,4971
Non-polymers7713
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)77.623, 77.623, 174.878
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number78
Cell settingtetragonal
Space group name H-MP43

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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.: 4
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-CO3 / CARBONATE ION


Mass: 60.009 Da / Num. of mol.: 4 / 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.: 4 / Source method: obtained synthetically / Formula: C14H20N6O5S
#4: Chemical
ChemComp-10A / DIDECYL-DIMETHYL-AMMONIUM


Mass: 326.623 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C22H48N
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 732 / 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: 2.03 Å3/Da / Density % sol: 39.3 %
Crystal growTemperature: 292 K / Method: evaporation / pH: 4.6
Details: PEG 4000, sodium acetate, ammonium acetate, SAH, DDDMAB, pH 4.6, EVAPORATION at 292K
Crystal grow
*PLUS
Temperature: 19 ℃ / Method: batch method
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
10.5-2 mMSAH11
20.100-0.200 mMDDDMAB11
37-10 mg/mlprotein11
48 %PEG400011
50.1 M11pH4.6CH3CO2Na
60.2 M11CH3CO2NH4

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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→30 Å / Num. all: 68170 / Num. obs: 68170 / % possible obs: 98 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.9 % / Biso Wilson estimate: 12.1 Å2 / Rsym value: 0.033 / Net I/σ(I): 29.4
Reflection shellResolution: 2→2.13 Å / Mean I/σ(I) obs: 20.8 / Rsym value: 0.081 / % possible all: 99
Reflection
*PLUS
Highest resolution: 2 Å / Lowest resolution: 30 Å / Num. measured all: 267466 / Rmerge(I) obs: 0.033
Reflection shell
*PLUS
% possible obs: 99 % / Rmerge(I) obs: 0.081

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
CNSphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 2→29.83 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 525398.94 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: CNS
RfactorNum. reflection% reflectionSelection details
Rfree0.24 6780 10.1 %RANDOM
Rwork0.194 ---
all0.194 67419 --
obs0.194 67419 97 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 45.9386 Å2 / ksol: 0.35688 e/Å3
Displacement parametersBiso mean: 22.5 Å2
Baniso -1Baniso -2Baniso -3
1-1.16 Å20 Å20 Å2
2--1.16 Å20 Å2
3----2.31 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.27 Å0.21 Å
Luzzati d res low-5 Å
Luzzati sigma a0.17 Å0.08 Å
Refinement stepCycle: LAST / Resolution: 2→29.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9059 0 210 732 10001
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d21.6
X-RAY DIFFRACTIONc_improper_angle_d0.74
X-RAY DIFFRACTIONc_mcbond_it1.311.5
X-RAY DIFFRACTIONc_mcangle_it2.022
X-RAY DIFFRACTIONc_scbond_it1.922
X-RAY DIFFRACTIONc_scangle_it2.692.5
LS refinement shellResolution: 2→2.13 Å / Rfactor Rfree error: 0.008 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.269 1131 10.1 %
Rwork0.198 10053 -
obs--96.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3SAH.PARSAH.TOP
X-RAY DIFFRACTION4LIP.PARLIP.TOP
X-RAY DIFFRACTION5CO3.PARCO3.TOP
Software
*PLUS
Name: CNS / Version: 1.1 / Classification: refinement
Refinement
*PLUS
σ(F): 2 / % reflection Rfree: 10.1 % / Rfactor Rfree: 0.24
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 22.5 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.0056
X-RAY DIFFRACTIONc_angle_deg1.25
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg21.6
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.74
X-RAY DIFFRACTIONc_mcbond_it1.311.5
X-RAY DIFFRACTIONc_scbond_it1.922
X-RAY DIFFRACTIONc_mcangle_it2.022
X-RAY DIFFRACTIONc_scangle_it2.692.5
LS refinement shell
*PLUS
Rfactor Rfree: 0.269 / % reflection Rfree: 10.1 % / Rfactor Rwork: 0.198

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