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- PDB-2fk8: Crystal structure of Hma (MmaA4) from Mycobacterium tuberculosis ... -

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Basic information

Entry
Database: PDB / ID: 2fk8
TitleCrystal structure of Hma (MmaA4) from Mycobacterium tuberculosis complexed with S-adenosylmethionine
Componentsmethoxy mycolic acid synthase 4
KeywordsTRANSFERASE / S-ADENOSYLMETHIONINE-DEPENDENT METHYLTRANSFERASE FOLD
Function / homology
Function and homology information


cyclopropane-fatty-acyl-phospholipid synthase activity / mycolic acid biosynthetic process / S-adenosylmethionine-dependent methyltransferase activity / lipid biosynthetic process / peptidoglycan-based cell wall / Transferases; Transferring one-carbon groups; Methyltransferases / methyltransferase activity / methylation / plasma membrane
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
S-ADENOSYLMETHIONINE / : / Hydroxymycolate synthase MmaA4
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsBoissier, F. / Guillet, V. / Mourey, L.
CitationJournal: J.Biol.Chem. / Year: 2006
Title: Further insight into S-adenosylmethionine-dependent methyltransferases: structural characterization of Hma, an enzyme essential for the biosynthesis of oxygenated mycolic acids in Mycobacterium tuberculosis.
Authors: Boissier, F. / Bardou, F. / Guillet, V. / Uttenweiler-Joseph, S. / Daffe, M. / Quemard, A. / Mourey, L.
History
DepositionJan 4, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 17, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Source and taxonomy / Version format compliance
Revision 1.3Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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: methoxy mycolic acid synthase 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,9202
Polymers36,5211
Non-polymers3981
Water2,756153
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)56.779, 56.779, 199.035
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
DetailsThe biological assembly is the monomer found in the asymmetric unit

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Components

#1: Protein methoxy mycolic acid synthase 4


Mass: 36521.305 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: H37Rv / Gene: mmaA4 (Rv0642c) / Plasmid: pET-15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS
References: GenBank: 13880191, UniProt: Q79FX8*PLUS, Transferases; Transferring one-carbon groups; Methyltransferases
#2: Chemical ChemComp-SAM / S-ADENOSYLMETHIONINE


Mass: 398.437 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H22N6O5S
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 153 / 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: 2.67 Å3/Da / Density % sol: 53.88 %
Crystal growTemperature: 285 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 4-28% PEG 3350, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 285.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.979171 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Dec 6, 2004 / Details: Toroidal mirror
RadiationMonochromator: Double crystal, Si(111) or Si(311) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979171 Å / Relative weight: 1
ReflectionResolution: 2→30 Å / Num. all: 25549 / Num. obs: 25549 / % possible obs: 97.7 % / Redundancy: 3.9 % / Biso Wilson estimate: 30.6 Å2 / Rsym value: 0.085 / Net I/σ(I): 4.8
Reflection shellResolution: 2→2.11 Å / Redundancy: 3.2 % / Mean I/σ(I) obs: 2.9 / Num. unique all: 3284 / Rsym value: 0.223 / % possible all: 88.1

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 2FK7

2fk7


Resolution: 2→30 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.921 / SU B: 6.911 / SU ML: 0.099 / TLS residual ADP flag: LIKELY RESIDUAL
Isotropic thermal model: isotropic + anisotropic in the last stages of refinement (TLS parameters were refined using a single group)
Cross valid method: THROUGHOUT / ESU R: 0.15 / ESU R Free: 0.155 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23889 1302 5.1 %RANDOM
Rwork0.17928 ---
all0.18214 24184 --
obs0.18214 24184 97.5 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 36.975 Å2
Baniso -1Baniso -2Baniso -3
1-0.52 Å20.26 Å20 Å2
2--0.52 Å20 Å2
3----0.78 Å2
Refinement stepCycle: LAST / Resolution: 2→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2236 0 27 153 2416
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0222319
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5391.9653146
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.555280
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.26923.54113
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.19715376
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.1811517
X-RAY DIFFRACTIONr_chiral_restr0.1140.2341
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021787
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2010.21063
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.310.21590
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.170.2136
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1830.221
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2020.26
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.9751.51454
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.48922263
X-RAY DIFFRACTIONr_scbond_it2.56631000
X-RAY DIFFRACTIONr_scangle_it3.9164.5883
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.304 93 -
Rwork0.201 1482 -
obs--83.07 %
Refinement TLS params.Method: refined / Origin x: 24.1462 Å / Origin y: -4.9533 Å / Origin z: 16.7397 Å
111213212223313233
T-0.1101 Å2-0.0615 Å2-0.0032 Å2--0.1127 Å20.0092 Å2---0.0881 Å2
L0.9274 °20.1372 °20.0944 °2-1.4665 °2-0.3333 °2--1.7997 °2
S0.0158 Å °-0.1336 Å °-0.0938 Å °0.0704 Å °0.0546 Å °-0.0361 Å °0.1114 Å °-0.0829 Å °-0.0704 Å °

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