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- PDB-2fk7: Crystal structure of Hma (MmaA4) from Mycobacterium tuberculosis,... -

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Basic information

Entry
Database: PDB / ID: 2fk7
TitleCrystal structure of Hma (MmaA4) from Mycobacterium tuberculosis, apo-form
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
: / Hydroxymycolate synthase MmaA4
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 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 1.3Nov 22, 2017Group: Database references / Category: pdbx_database_related
Revision 1.4Aug 30, 2023Group: Data collection / Database references / 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: methoxy mycolic acid synthase 4


Theoretical massNumber of molelcules
Total (without water)36,5211
Polymers36,5211
Non-polymers00
Water2,234124
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)56.715, 56.715, 206.220
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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 124 / 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: 2.76 Å3/Da / Density % sol: 55.38 %
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: ID14-3 / Wavelength: 0.931 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Nov 4, 2004 / Details: Toroidal mirror
RadiationMonochromator: Diamond (111), Ge(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.931 Å / Relative weight: 1
ReflectionResolution: 2.1→44.3 Å / Num. all: 22776 / Num. obs: 22776 / % possible obs: 97.5 % / Redundancy: 9.7 % / Biso Wilson estimate: 42.3 Å2 / Rsym value: 0.1 / Net I/σ(I): 3.8
Reflection shellResolution: 2.1→2.21 Å / Redundancy: 10 % / Mean I/σ(I) obs: 3.7 / Num. unique all: 3315 / Rsym value: 0.186 / % possible all: 100

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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 1KP9

1kp9


Resolution: 2.1→30 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.928 / SU B: 8.445 / SU ML: 0.116 / 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: 0.185 / ESU R Free: 0.165 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23226 1173 5.2 %RANDOM
Rwork0.19546 ---
all0.19734 21535 --
obs0.19734 21535 97.05 %-
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: 65.44 Å2
Baniso -1Baniso -2Baniso -3
1-0.55 Å20.27 Å20 Å2
2--0.55 Å20 Å2
3----0.82 Å2
Refinement stepCycle: LAST / Resolution: 2.1→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2218 0 0 124 2342
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.0222271
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.7361.9533076
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8545275
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.04723.482112
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.79515378
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.7231517
X-RAY DIFFRACTIONr_chiral_restr0.1320.2333
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021749
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2110.21044
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3170.21564
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1230.2139
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1110.237
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2350.27
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.1761.51448
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.63622227
X-RAY DIFFRACTIONr_scbond_it2.7883972
X-RAY DIFFRACTIONr_scangle_it3.954.5849
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.1→2.154 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.26 86 -
Rwork0.207 1570 -
obs--100 %
Refinement TLS params.Method: refined / Origin x: 25.4802 Å / Origin y: 7.9661 Å / Origin z: 16.6698 Å
111213212223313233
T-0.2665 Å2-0.028 Å2-0.0105 Å2--0.3381 Å2-0.0234 Å2---0.3243 Å2
L1.1806 °2-0.2999 °2-0.5293 °2-2.773 °20.1309 °2--3.622 °2
S-0.1961 Å °-0.0416 Å °0.1041 Å °-0.1965 Å °0.3472 Å °-0.1513 Å °-0.4255 Å °-0.1731 Å °-0.1511 Å °

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