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- PDB-3ha3: Crystal structure of HMA (MMAA4) from mycobacterium tuberculosis ... -

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Basic information

Entry
Database: PDB / ID: 3ha3
TitleCrystal structure of HMA (MMAA4) from mycobacterium tuberculosis complexed with S-adenosylhomocysteine
ComponentsMETHOXY MYCOLIC ACID SYNTHASE 4
KeywordsTRANSFERASE / S-ADENOSYLMETHIONINE-DEPENDENT METHYLTRANSFERASE FOLD / Methyltransferase
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-ADENOSYL-L-HOMOCYSTEINE / Hydroxymycolate synthase MmaA4
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.2 Å
AuthorsBoissier, F. / Vaubourgeix, J. / Julien, S. / Mourey, L.
CitationJournal: To be Published
Title: SADAE, a potent bisubstrate inhibitor of mycobacterium tuberculosis mycolic acid methyltransferases
Authors: Vaubourgeix, J. / Bardou, F. / Boissier, F. / Julien, S. / Constant, P. / Ploux, O. / Daffe, M. / Quemard, A. / Mourey, L.
History
DepositionMay 1, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 12, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Sep 6, 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

Downloads & links

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Assembly

Deposited unit
A: METHOXY MYCOLIC ACID SYNTHASE 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,9062
Polymers36,5211
Non-polymers3841
Water1,13563
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)57.344, 57.344, 203.978
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein METHOXY MYCOLIC ACID SYNTHASE 4 / MMAA4 (METHYL MYCOLIC ACID SYNTHASE 4) (MMA4) (HYDROXY MYCOLIC ACID SYNTHASE)


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, MMAA4 (RV0642C), Rv0642c / Plasmid: PET-15B / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)PLYSS
References: UniProt: Q79FX8, Transferases; Transferring one-carbon groups; Methyltransferases
#2: Chemical ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE


Type: L-peptide linking / Mass: 384.411 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H20N6O5S
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 63 / 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: 2.5 Å3/Da / Density % sol: 50.81 %
Crystal growTemperature: 285 K / Method: vapor diffusion, hanging drop
Details: 4-28% PEG 3350, pH 5-9, VAPOR DIFFUSION, HANGING DROP, temperature 285K
PH range: 5-9

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Sep 22, 2005
RadiationMonochromator: Diamond monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 2.2→28.68 Å / Num. all: 20193 / Num. obs: 20193 / % possible obs: 98.4 % / Redundancy: 3.4 % / Biso Wilson estimate: 44.1 Å2 / Rsym value: 0.047 / Net I/σ(I): 9.1
Reflection shellResolution: 2.2→2.32 Å / Redundancy: 3.4 % / Mean I/σ(I) obs: 2.4 / Num. unique all: 2844 / Rsym value: 0.301 / % possible all: 97.8

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB ENTRY 2FK8

2fk8


Resolution: 2.2→28.68 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.924 / SU B: 11.326 / SU ML: 0.144 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.223 / ESU R Free: 0.197 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25001 1031 5.1 %RANDOM
Rwork0.20164 ---
obs0.20399 19162 97.82 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 57.076 Å2
Baniso -1Baniso -2Baniso -3
1-0.03 Å20.02 Å20 Å2
2--0.03 Å20 Å2
3----0.05 Å2
Refinement stepCycle: LAST / Resolution: 2.2→28.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2256 0 26 63 2345
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0222340
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6741.9663172
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1575280
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.85323.534116
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.76315384
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.1761517
X-RAY DIFFRACTIONr_chiral_restr0.1140.2341
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021805
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2180.21101
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3150.21607
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1360.2113
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1390.223
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3210.24
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.0031.51457
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.62322267
X-RAY DIFFRACTIONr_scbond_it2.57131028
X-RAY DIFFRACTIONr_scangle_it3.8254.5905
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.294 78 -
Rwork0.241 1354 -
obs--96.82 %
Refinement TLS params.Method: refined / Origin x: 25.5935 Å / Origin y: 6.9993 Å / Origin z: 16.5489 Å
111213212223313233
T-0.0663 Å20.073 Å20.0037 Å2--0.1017 Å20.0087 Å2---0.0636 Å2
L0.5635 °2-0.179 °2-0.3885 °2-1.2367 °20.1013 °2--1.774 °2
S-0.0828 Å °0.0466 Å °0.1087 Å °0.0597 Å °0.2085 Å °-0.0976 Å °-0.124 Å °-0.1219 Å °-0.1257 Å °

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