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

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Basic information

Entry
Database: PDB / ID: 1kpg
TitleCrystal Structure of mycolic acid cyclopropane synthase CmaA1 complexed with SAH and CTAB
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
CETYL-TRIMETHYL-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 / MAD / 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 1.3Nov 20, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ref_seq_dif / struct_site
Item: _chem_comp.mon_nstd_flag / _chem_comp.type ..._chem_comp.mon_nstd_flag / _chem_comp.type / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _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 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)134,78016
Polymers131,8654
Non-polymers2,91612
Water11,800655
1
A: CYCLOPROPANE-FATTY-ACYL-PHOSPHOLIPID SYNTHASE 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,6954
Polymers32,9661
Non-polymers7293
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)33,6954
Polymers32,9661
Non-polymers7293
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)33,6954
Polymers32,9661
Non-polymers7293
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)33,6954
Polymers32,9661
Non-polymers7293
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)77.323, 77.323, 173.490
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: 32966.125 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


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


Mass: 284.543 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C19H42N
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 655 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 1.97 Å3/Da / Density % sol: 37.45 %
Crystal growTemperature: 292 K / Method: evaporation / pH: 4.6
Details: PEG 4000, sodium acetate, ammonium acetate, SAH, CTAB, 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 mMCTAB11
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-D / Wavelength: 0.9790, 0.9793, 0.9638
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 10, 2001
RadiationMonochromator: bent cylindrical Si-mirror (Rh coating), Si(111) double-crystal monochromator
Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.9791
20.97931
30.96381
ReflectionResolution: 2→30 Å / Num. all: 133048 / Num. obs: 133048 / % possible obs: 97.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.3 % / Biso Wilson estimate: 10.4 Å2 / Rsym value: 0.069 / Net I/σ(I): 9
Reflection shellResolution: 2→2.13 Å / Mean I/σ(I) obs: 3.7 / Rsym value: 0.199 / % possible all: 86
Reflection
*PLUS
Lowest resolution: 30 Å / Num. measured all: 442646 / Rmerge(I) obs: 0.069
Reflection shell
*PLUS
% possible obs: 86 % / Rmerge(I) obs: 0.199

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
SHARPphasing
CNS1.1refinement
RefinementMethod to determine structure: MAD / Resolution: 2→29.68 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 102136.86 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: CNS
RfactorNum. reflection% reflectionSelection details
Rfree0.233 6616 10.1 %RANDOM
Rwork0.191 ---
all0.19 65678 --
obs0.191 65678 95.9 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 34.6467 Å2 / ksol: 0.29153 e/Å3
Displacement parametersBiso mean: 19.8 Å2
Baniso -1Baniso -2Baniso -3
1-1.46 Å20 Å20 Å2
2--1.46 Å20 Å2
3----2.93 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.27 Å0.21 Å
Luzzati d res low-5 Å
Luzzati sigma a0.21 Å0.14 Å
Refinement stepCycle: LAST / Resolution: 2→29.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9051 0 200 655 9906
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_d21.7
X-RAY DIFFRACTIONc_improper_angle_d0.77
X-RAY DIFFRACTIONc_mcbond_it1.291.5
X-RAY DIFFRACTIONc_mcangle_it1.922
X-RAY DIFFRACTIONc_scbond_it2.042
X-RAY DIFFRACTIONc_scangle_it2.822.5
LS refinement shellResolution: 2→2.13 Å / Rfactor Rfree error: 0.009 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.269 920 9.5 %
Rwork0.211 8748 -
obs--84.7 %
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 DIFFRACTION4CTA.PARCTA.TOP
X-RAY DIFFRACTION5CO3.PARCO3.TOP
Software
*PLUS
Name: CNS / Version: 1.1 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 30 Å / σ(F): 0 / % reflection Rfree: 10 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 19.8 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.0057
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg21.7
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.77
X-RAY DIFFRACTIONc_mcbond_it1.291.5
X-RAY DIFFRACTIONc_scbond_it2.042
X-RAY DIFFRACTIONc_mcangle_it1.922
X-RAY DIFFRACTIONc_scangle_it2.822.5
LS refinement shell
*PLUS
Rfactor Rfree: 0.269 / % reflection Rfree: 9.5 % / Rfactor Rwork: 0.211

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