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- PDB-6jcl: Crystal structure of cofactor-bound Rv0187 from MTB -

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Basic information

Entry
Database: PDB / ID: 6jcl
TitleCrystal structure of cofactor-bound Rv0187 from MTB
ComponentsProbable O-methyltransferase
KeywordsMETAL BINDING PROTEIN / methyltransferase
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
S-ADENOSYL-L-HOMOCYSTEINE / STRONTIUM ION / Catechol O-methyltransferase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.644 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 ...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 / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Probable O-methyltransferase
B: Probable O-methyltransferase
C: Probable O-methyltransferase
D: Probable O-methyltransferase
G: Probable O-methyltransferase
H: Probable O-methyltransferase
E: Probable O-methyltransferase
F: Probable O-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)204,35236
Polymers199,3148
Non-polymers5,03828
Water15,727873
1
A: Probable O-methyltransferase
B: Probable O-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,41313
Polymers49,8282
Non-polymers1,58411
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5430 Å2
ΔGint-152 kcal/mol
Surface area17090 Å2
MethodPISA
2
C: Probable O-methyltransferase
D: Probable O-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,0098
Polymers49,8282
Non-polymers1,1806
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4980 Å2
ΔGint-136 kcal/mol
Surface area16730 Å2
MethodPISA
3
G: Probable O-methyltransferase
H: Probable O-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,0969
Polymers49,8282
Non-polymers1,2687
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5040 Å2
ΔGint-134 kcal/mol
Surface area16530 Å2
MethodPISA
4
E: Probable O-methyltransferase
F: Probable O-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,8346
Polymers49,8282
Non-polymers1,0054
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5040 Å2
ΔGint-135 kcal/mol
Surface area16420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.300, 75.920, 329.839
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
11(chain A and (resid 4 through 15 or resid 17...
21(chain B and ((resid 4 and (name N or name...
31(chain C and (resid 4 through 15 or resid 17...
41(chain D and ((resid 4 and (name N or name...
51(chain E and ((resid 4 and (name N or name...
61(chain F and (resid 4 through 15 or resid 17...
71(chain G and (resid 4 through 15 or resid 17...
81(chain H and (resid 4 through 15 or resid 17...

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain A and (resid 4 through 15 or resid 17...A4 - 15
121(chain A and (resid 4 through 15 or resid 17...A17 - 20
131(chain A and (resid 4 through 15 or resid 17...A3 - 220
141(chain A and (resid 4 through 15 or resid 17...A30 - 57
151(chain A and (resid 4 through 15 or resid 17...A58 - 60
161(chain A and (resid 4 through 15 or resid 17...A3 - 220
171(chain A and (resid 4 through 15 or resid 17...A3 - 220
181(chain A and (resid 4 through 15 or resid 17...A3 - 220
191(chain A and (resid 4 through 15 or resid 17...A3 - 220
211(chain B and ((resid 4 and (name N or name...B4
221(chain B and ((resid 4 and (name N or name...B4 - 220
231(chain B and ((resid 4 and (name N or name...B4 - 220
241(chain B and ((resid 4 and (name N or name...B4 - 220
251(chain B and ((resid 4 and (name N or name...B4 - 220
311(chain C and (resid 4 through 15 or resid 17...C4 - 15
321(chain C and (resid 4 through 15 or resid 17...C17 - 20
331(chain C and (resid 4 through 15 or resid 17...C22 - 28
341(chain C and (resid 4 through 15 or resid 17...C3 - 218
351(chain C and (resid 4 through 15 or resid 17...C3 - 218
361(chain C and (resid 4 through 15 or resid 17...C3 - 218
371(chain C and (resid 4 through 15 or resid 17...C3 - 218
381(chain C and (resid 4 through 15 or resid 17...C3 - 218
411(chain D and ((resid 4 and (name N or name...D4
421(chain D and ((resid 4 and (name N or name...D4 - 218
431(chain D and ((resid 4 and (name N or name...D4 - 218
441(chain D and ((resid 4 and (name N or name...D4 - 218
451(chain D and ((resid 4 and (name N or name...D4 - 218
511(chain E and ((resid 4 and (name N or name...E4
521(chain E and ((resid 4 and (name N or name...E4 - 220
531(chain E and ((resid 4 and (name N or name...E4 - 220
541(chain E and ((resid 4 and (name N or name...E4 - 220
551(chain E and ((resid 4 and (name N or name...E4 - 220
611(chain F and (resid 4 through 15 or resid 17...F4 - 15
621(chain F and (resid 4 through 15 or resid 17...F17 - 20
631(chain F and (resid 4 through 15 or resid 17...F22 - 28
641(chain F and (resid 4 through 15 or resid 17...F30 - 57
651(chain F and (resid 4 through 15 or resid 17...F3 - 218
661(chain F and (resid 4 through 15 or resid 17...F3 - 218
671(chain F and (resid 4 through 15 or resid 17...F3 - 218
681(chain F and (resid 4 through 15 or resid 17...F3 - 218
691(chain F and (resid 4 through 15 or resid 17...F3 - 218
711(chain G and (resid 4 through 15 or resid 17...G4 - 15
721(chain G and (resid 4 through 15 or resid 17...G17 - 20
731(chain G and (resid 4 through 15 or resid 17...G22 - 28
741(chain G and (resid 4 through 15 or resid 17...G30 - 57
751(chain G and (resid 4 through 15 or resid 17...G3 - 303
761(chain G and (resid 4 through 15 or resid 17...G3 - 303
771(chain G and (resid 4 through 15 or resid 17...G3 - 303
781(chain G and (resid 4 through 15 or resid 17...G3 - 303
791(chain G and (resid 4 through 15 or resid 17...G3 - 303
811(chain H and (resid 4 through 15 or resid 17...H4 - 15
821(chain H and (resid 4 through 15 or resid 17...H17 - 20
831(chain H and (resid 4 through 15 or resid 17...H22 - 28
841(chain H and (resid 4 through 15 or resid 17...H30 - 57
851(chain H and (resid 4 through 15 or resid 17...H4 - 219
861(chain H and (resid 4 through 15 or resid 17...H4 - 219
871(chain H and (resid 4 through 15 or resid 17...H4 - 219
881(chain H and (resid 4 through 15 or resid 17...H4 - 219
891(chain H and (resid 4 through 15 or resid 17...H4 - 219

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Components

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Protein , 1 types, 8 molecules ABCDGHEF

#1: Protein
Probable O-methyltransferase


Mass: 24914.230 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (bacteria)
Strain: ATCC 25618 / H37Rv / Gene: Rv0187 / Plasmid: pLATE31 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: O07431

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Non-polymers , 5 types, 901 molecules

#2: Chemical
ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE


Type: L-peptide linking / Mass: 384.411 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C14H20N6O5S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-SR / STRONTIUM ION


Mass: 87.620 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: Sr / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 873 / 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: 2.37 Å3/Da / Density % sol: 47.99 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: 0.22mM Rv0187, 2mM SAH and 2.6mM MgCl2 0.1 M HEPES pH 7.3 70% v/v (+/-)-2-Methyl-2,4-pentanediol 0.1M Strontium chloride hexahydrate

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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: Oct 8, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.64→62.47 Å / Num. obs: 227245 / % possible obs: 98.9 % / Redundancy: 14.4 % / Biso Wilson estimate: 21.32 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.148 / Rpim(I) all: 0.04 / Rrim(I) all: 0.153 / Net I/σ(I): 13.4
Reflection shellResolution: 1.64→1.67 Å / Redundancy: 12.4 % / Rmerge(I) obs: 2.442 / Num. unique obs: 10420 / CC1/2: 0.303 / Rpim(I) all: 0.706 / Rrim(I) all: 2.548 / % possible all: 92.7

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
SCALA0.7.3data scaling
PDB_EXTRACT3.24data extraction
iMOSFLMdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6JCM

6jcm


Resolution: 1.644→36.232 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 21.38
RfactorNum. reflection% reflection
Rfree0.2069 11295 4.98 %
Rwork0.1808 --
obs0.1821 227000 98.63 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 99.27 Å2 / Biso mean: 35.4007 Å2 / Biso min: 13.45 Å2
Refinement stepCycle: final / Resolution: 1.644→36.232 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12644 0 291 873 13808
Biso mean--31.72 39.51 -
Num. residues----1734
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A4116X-RAY DIFFRACTION13.272TORSIONAL
12B4116X-RAY DIFFRACTION13.272TORSIONAL
13C4116X-RAY DIFFRACTION13.272TORSIONAL
14D4116X-RAY DIFFRACTION13.272TORSIONAL
15E4116X-RAY DIFFRACTION13.272TORSIONAL
16F4116X-RAY DIFFRACTION13.272TORSIONAL
17G4116X-RAY DIFFRACTION13.272TORSIONAL
18H4116X-RAY DIFFRACTION13.272TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.644-1.66270.34183570.32546403676090
1.6627-1.68220.33383750.30976917729296
1.6822-1.70280.32833350.2967115745098
1.7028-1.72430.30893460.2887160750698
1.7243-1.7470.29163380.26947081741998
1.747-1.77090.28713690.267067743698
1.7709-1.79620.27363840.24347112749698
1.7962-1.8230.26383620.23347106746898
1.823-1.85150.25783970.22787130752799
1.8515-1.88190.27473520.23047181753399
1.8819-1.91430.27173740.24217065743999
1.9143-1.94910.26963660.24817206757299
1.9491-1.98660.22294020.20057119752199
1.9866-2.02720.22823670.1937160752799
2.0272-2.07130.22723640.20557147751199
2.0713-2.11940.21363680.18557210757899
2.1194-2.17240.22024050.17447199760499
2.1724-2.23120.21754320.17637179761199
2.2312-2.29680.20923990.1787145754499
2.2968-2.37090.19163950.16687242763799
2.3709-2.45560.19663720.17357223759599
2.4556-2.55390.23670.16987269763699
2.5539-2.67010.20063340.158473197653100
2.6701-2.81090.18123290.16173857714100
2.8109-2.98690.19953750.172472607635100
2.9869-3.21740.18773600.169773597719100
3.2174-3.54090.18974320.161973317763100
3.5409-4.05270.17343900.148574037793100
4.0527-5.10370.16673890.147175227911100
5.1037-36.24050.19724600.17837690815099
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)
11.5115-0.1441-0.02061.4003-0.22750.98650.06590.26280.0936-0.0375-0.04080.0805-0.09380.0157-0.03240.07640.00010.02190.2877-0.00170.189115.37037.5734-74.3072
21.7911-0.335-0.28261.51270.25111.03270.03840.2447-0.1778-0.0111-0.10030.02430.16060.05430.05360.08010.01730.0110.2933-0.03350.226.5702-15.4887-73.9994
31.6110.25160.11810.7699-0.19561.2971-0.0440.13920.06770.12610.14360.2048-0.2118-0.327-0.06140.14890.0680.05970.23580.04290.1988-7.921915.2573-56.4807
40.5142-0.0737-0.46040.9109-0.02820.85570.1299-0.18870.24550.76050.0220.1227-0.7846-0.1512-0.1270.74680.14030.14890.2787-0.02510.2642-4.674225.9637-33.086
50.6323-0.4721-0.12820.47270.41860.9926-0.3169-0.14570.0420.72110.2438-0.1796-0.15740.16150.05460.8220.0055-0.06320.2813-0.03660.215426.9204-2.7264-8.4658
60.2531-0.2348-0.11290.26360.12730.7746-0.318-0.1396-0.03780.66950.19010.276-0.3746-0.2936-0.03081.05790.1470.27560.3249-0.02460.02113.0256.6236-8.572
71.99990.42-0.12061.5753-0.041.67210.06280.1737-0.15840.0778-0.0305-0.25590.38670.3463-0.0110.21440.0862-0.03050.22290.00730.168846.4315-22.0547-49.3166
80.4539-0.0081-0.05641.299-0.75311.6470.1362-0.1614-0.09960.3842-0.1024-0.00030.583-0.049-0.02110.5169-0.0764-0.03990.2280.02010.182135.5564-25.9147-26.0287
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resseq 5:222)A5 - 222
2X-RAY DIFFRACTION2(chain B and resseq 6:222)B6 - 222
3X-RAY DIFFRACTION3(chain C and resseq 5:220)C5 - 220
4X-RAY DIFFRACTION4(chain D and resseq 6:220)D6 - 220
5X-RAY DIFFRACTION5(chain G and resseq 5:223)G5 - 223
6X-RAY DIFFRACTION6(chain H and resseq 6:221)H6 - 221
7X-RAY DIFFRACTION7(chain E and resseq 6:222)E6 - 222
8X-RAY DIFFRACTION8(chain F and resseq 5:220)F5 - 220

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