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- PDB-6jcm: Crystal structure of ligand-free Rv0187. -

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Basic information

Entry
Database: PDB / ID: 6jcm
TitleCrystal structure of ligand-free Rv0187.
ComponentsProbable O-methyltransferase
KeywordsTRANSFERASE / O-Methyltransferase / MTB / COMT / Rossmann
Function / homology
Function and homology information


catechol O-methyltransferase activity / : / : / catechol O-methyltransferase / S-adenosylmethionine-dependent methyltransferase activity / methylation / metal ion binding / plasma membrane
Similarity search - Function
O-methyltransferase / Class I-like SAM-dependent O-methyltransferase / SAM-dependent O-methyltransferase class I-type profile. / Vaccinia Virus protein VP39 / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / Catechol O-methyltransferase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.08 Å
AuthorsKim, J. / Lee, S.
Funding support Korea, Republic Of, 1items
OrganizationGrant numberCountry
National Research Foundation (Korea)2016R1D1A1B03930716 Korea, Republic Of
CitationJournal: Sci Rep / Year: 2019
Title: Structural and biochemical characterization of Rv0187, an O-methyltransferase from Mycobacterium tuberculosis.
Authors: Lee, S. / Kang, J. / Kim, J.
History
DepositionJan 29, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 11, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 22, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Probable O-methyltransferase
B: Probable O-methyltransferase
C: Probable O-methyltransferase
D: Probable O-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,7748
Polymers104,5384
Non-polymers2364
Water1,910106
1
A: Probable O-methyltransferase
B: Probable O-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,3874
Polymers52,2692
Non-polymers1182
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4260 Å2
ΔGint-40 kcal/mol
Surface area16340 Å2
MethodPISA
2
C: Probable O-methyltransferase
D: Probable O-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,3874
Polymers52,2692
Non-polymers1182
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4300 Å2
ΔGint-40 kcal/mol
Surface area16190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.333, 94.262, 125.677
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14B
24C
15B
25D
16C
26D

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1010A4 - 218
2010B4 - 218
1020A4 - 218
2020C4 - 218
1030A4 - 218
2030D4 - 218
1040B4 - 218
2040C4 - 218
1050B4 - 218
2050D4 - 218
1060C4 - 218
2060D4 - 218

NCS ensembles :
ID
1
2
3
4
5
6

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Components

#1: Protein
Probable O-methyltransferase


Mass: 26134.555 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (bacteria)
Strain: ATCC 25618 / H37Rv / Gene: Rv0187 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: O07431
#2: Chemical
ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H3O2
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 106 / 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: 2.3 Å3/Da / Density % sol: 46.62 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / Details: Sodium acetate trihydrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 0.9793 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: May 19, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.08→50 Å / Num. obs: 57861 / % possible obs: 98.7 % / Redundancy: 7 % / Rmerge(I) obs: 0.243 / Rpim(I) all: 0.098 / Rrim(I) all: 0.263 / Χ2: 2.247 / Net I/σ(I): 5.3
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.08-2.126.11.74928090.4770.7351.9041.57297.9
2.12-2.157.11.57128590.5490.6211.6931.56898.6
2.15-2.27.41.19428550.6840.4641.2841.6798.5
2.2-2.247.41.10328420.730.431.1861.7298.3
2.24-2.297.41.03228490.7680.4021.111.76598.5
2.29-2.347.30.86328680.8290.3370.9291.77698.7
2.34-2.47.30.79628480.8010.3110.8571.80798.6
2.4-2.477.20.79428730.820.3130.8551.83298.5
2.47-2.547.20.65928720.8650.260.711.88698.4
2.54-2.627.20.50128460.9250.1980.541.92398.6
2.62-2.717.10.41928720.9460.1660.4522.06998.6
2.71-2.827.10.37228780.9570.1480.4012.08898.6
2.82-2.9570.30128640.9650.120.3242.23298
2.95-3.116.90.2428880.9790.0960.2592.40398.4
3.11-3.36.80.20328700.9840.0820.222.60898.2
3.3-3.566.60.15229070.9910.0620.1652.96598.5
3.56-3.916.50.12229370.9940.0510.1333.33899.2
3.91-4.486.50.10429790.9960.0440.1133.49899.8
4.48-5.6470.09629970.9970.0390.1043.28599.9
5.64-506.80.08431480.9960.0350.0913.08299

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
HKL-2000data scaling
PDB_EXTRACT3.24data extraction
HKL-2000data reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3dul

3dul


Resolution: 2.08→29.24 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.939 / SU B: 4.604 / SU ML: 0.121 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.202 / ESU R Free: 0.168 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2306 2966 5.1 %RANDOM
Rwork0.2034 ---
obs0.2048 54831 98.56 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 85.58 Å2 / Biso mean: 26.919 Å2 / Biso min: 12.67 Å2
Baniso -1Baniso -2Baniso -3
1--0.16 Å20 Å20 Å2
2---0.43 Å20 Å2
3---0.59 Å2
Refinement stepCycle: final / Resolution: 2.08→29.24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6276 0 16 106 6398
Biso mean--29.58 25.78 -
Num. residues----860
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0136392
X-RAY DIFFRACTIONr_bond_other_d0.0010.0176165
X-RAY DIFFRACTIONr_angle_refined_deg1.5361.638721
X-RAY DIFFRACTIONr_angle_other_deg1.4011.57514111
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5185856
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.7620.712323
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.37615940
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.7691562
X-RAY DIFFRACTIONr_chiral_restr0.0810.2852
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.027412
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021362
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A62830.1
12B62830.1
21A64260.05
22C64260.05
31A63490.09
32D63490.09
41B63030.09
42C63030.09
51B63730.06
52D63730.06
61C63280.08
62D63280.08
LS refinement shellResolution: 2.081→2.135 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.331 241 -
Rwork0.279 3907 -
all-4148 -
obs--96.85 %

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