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- PDB-2ckd: Crystal structure of ML2640 from Mycobacterium leprae -

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Basic information

Entry
Database: PDB / ID: 2ckd
TitleCrystal structure of ML2640 from Mycobacterium leprae
ComponentsPUTATIVE S-ADENOSYL-L-METHIONINE-DEPENDENT METHYLTRANSFERASE ML2640
KeywordsTRANSFERASE
Function / homology
Function and homology information


Transferases; Transferring one-carbon groups; Methyltransferases / methyltransferase activity / methylation
Similarity search - Function
S-adenosyl-L-methionine-dependent methyltransferase, putative / Methyltransferase Ppm1/Ppm2/Tcmp / Leucine carboxyl methyltransferase / Vaccinia Virus protein VP39 / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Putative S-adenosyl-L-methionine-dependent methyltransferase ML2640
Similarity search - Component
Biological speciesMYCOBACTERIUM LEPRAE (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsGrana, M. / Buschiazzo, A. / Wehenkel, A. / Haouz, A. / Alzari, P.M.
CitationJournal: Protein Sci. / Year: 2007
Title: The Crystal Structure of M. Leprae Ml2640C Defines a Large Family of Putative S-Adenosylmethionine- Dependent Methyltransferases in Mycobacteria.
Authors: Grana, M. / Haouz, A. / Buschiazzo, A. / Miras, I. / Wehenkel, A. / Bondet, V. / Shepard, W. / Schaeffer, F. / Cole, S.T. / Alzari, P.M.
History
DepositionApr 17, 2006Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 29, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Refinement description / Version format compliance
Revision 1.2May 1, 2024Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PUTATIVE S-ADENOSYL-L-METHIONINE-DEPENDENT METHYLTRANSFERASE ML2640
B: PUTATIVE S-ADENOSYL-L-METHIONINE-DEPENDENT METHYLTRANSFERASE ML2640


Theoretical massNumber of molelcules
Total (without water)68,9852
Polymers68,9852
Non-polymers00
Water00
1
A: PUTATIVE S-ADENOSYL-L-METHIONINE-DEPENDENT METHYLTRANSFERASE ML2640


Theoretical massNumber of molelcules
Total (without water)34,4931
Polymers34,4931
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: PUTATIVE S-ADENOSYL-L-METHIONINE-DEPENDENT METHYLTRANSFERASE ML2640


Theoretical massNumber of molelcules
Total (without water)34,4931
Polymers34,4931
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)96.780, 96.780, 169.367
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein PUTATIVE S-ADENOSYL-L-METHIONINE-DEPENDENT METHYLTRANSFERASE ML2640 / HYPOTHETICAL PROTEIN ML2640


Mass: 34492.656 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MYCOBACTERIUM LEPRAE (bacteria) / Plasmid: PDEST17 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21
References: UniProt: Q9CCZ4, Transferases; Transferring one-carbon groups; Methyltransferases

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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: 2.9 Å3/Da / Density % sol: 56 %
Description: THE STRUCTURE WAS DETERMINED AT 3 A RESOLUTION USING SAD PHASING FROM A SEMET-LABELED CRYSTAL. THIS DATASET CORRESPONDS TO THE WILD-TYPE NON-LABELED PROTEIN
Crystal growpH: 7.5
Details: 1.6 M AMMONIUM SULFATE, 0.1 M HEPES, PH 7.5, 50 MM MGCL2 (PROTEIN CONCENTRATION 11.8 MG/ML)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.9792
DetectorType: ADSC QUANTUM-210 / Detector: CCD / Date: Oct 14, 2003
RadiationMonochromator: SILICON 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.8→85 Å / Num. obs: 20669 / % possible obs: 99.6 % / Observed criterion σ(I): 0 / Redundancy: 5.5 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 8
Reflection shellResolution: 2.8→2.95 Å / Redundancy: 5.6 % / Rmerge(I) obs: 0.25 / Mean I/σ(I) obs: 3 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PREVIOUS MODEL OBTAINED FROM SAD PHASING

Resolution: 2.8→83.92 Å / Cor.coef. Fo:Fc: 0.929 / Cor.coef. Fo:Fc free: 0.88 / SU B: 29.887 / SU ML: 0.258 / TLS residual ADP flag: UNVERIFIED / Cross valid method: THROUGHOUT / ESU R: 1.634 / ESU R Free: 0.358 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. TWO PROTEIN LOOPS AND A FEW SOLVENT- EXPOSED SIDE-CHAINS WERE MODELED STEREOCHEMICALLY.
RfactorNum. reflection% reflectionSelection details
Rfree0.255 1043 5.1 %RANDOM
Rwork0.199 ---
obs0.202 19338 99.3 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 12.37 Å2
Baniso -1Baniso -2Baniso -3
1--0.49 Å20 Å20 Å2
2---0.49 Å20 Å2
3---0.98 Å2
Refinement stepCycle: LAST / Resolution: 2.8→83.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4692 0 0 0 4692
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0224800
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.8261.9386542
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.1615599
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.97322.949234
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.30215741
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.3821550
X-RAY DIFFRACTIONr_chiral_restr0.1240.2721
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.023752
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2480.22143
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3270.23250
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1490.2158
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1980.250
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1750.28
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.7651.53059
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.29324798
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.96931999
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.1914.51744
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.8→2.87 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.393 72
Rwork0.313 1410
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.2902-0.5308-0.69041.5787-0.09882.63120.07570.10230.3962-0.1950.05310.1017-0.3137-0.1064-0.1288-0.17870.0372-0.0586-0.12870.0009-0.0745-12.0435-33.220326.613
21.2142-1.03030.96232.3632-0.15583.72540.1510.1034-0.4784-0.15280.04510.4640.4306-0.3969-0.1961-0.1365-0.0265-0.0041-0.15410.0029-0.0427-1.381-67.274147.8619
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A8 - 310
2X-RAY DIFFRACTION2B12 - 310

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