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- PDB-6lyh: Crystal structure of tea N9-methyltransferase CkTcS in complex wi... -

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Basic information

Entry
Database: PDB / ID: 6lyh
TitleCrystal structure of tea N9-methyltransferase CkTcS in complex with SAH and 1,3,7-trimethyluric acid
ComponentsN-methyltransferase CkTcS
KeywordsTRANSFERASE / N-methyltransferase / CkTcS
Function / homology
Function and homology information


caffeine synthase / theobromine:S-adenosyl-L-methionine 1-N-methyltransferase activity / paraxanthine:S-adenosyl-L-methionine 3-N-methyltransferase activity / alkaloid metabolic process / methylation / metal ion binding
Similarity search - Function
Methyltransferase, alpha-helical capping domain / SAM dependent carboxyl methyltransferase / SAM dependent carboxyl methyltransferase / S-adenosyl-L-methionine-dependent methyltransferase superfamily
Similarity search - Domain/homology
1,3,7-trimethyl-9H-purine-2,6,8-trione / S-ADENOSYL-L-HOMOCYSTEINE / 3,7-dimethylxanthine N-methyltransferase TCS1
Similarity search - Component
Biological speciesCamellia sinensis var. assamica (Assam tea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.15000316024 Å
AuthorsWang, Y. / Zhang, Z.-M.
CitationJournal: Nat Commun / Year: 2020
Title: Identification and characterization of N9-methyltransferase involved in converting caffeine into non-stimulatory theacrine in tea.
Authors: Zhang, Y.H. / Li, Y.F. / Wang, Y. / Tan, L. / Cao, Z.Q. / Xie, C. / Xie, G. / Gong, H.B. / Sun, W.Y. / Ouyang, S.H. / Duan, W.J. / Lu, X. / Ding, K. / Kurihara, H. / Hu, D. / Zhang, Z.M. / Abe, I. / He, R.R.
History
DepositionFeb 14, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 4, 2020Provider: repository / Type: Initial release
Revision 1.1Apr 1, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Nov 29, 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

Downloads & links

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Assembly

Deposited unit
B: N-methyltransferase CkTcS
A: N-methyltransferase CkTcS
C: N-methyltransferase CkTcS
D: N-methyltransferase CkTcS
E: N-methyltransferase CkTcS
F: N-methyltransferase CkTcS
G: N-methyltransferase CkTcS
H: N-methyltransferase CkTcS
hetero molecules


Theoretical massNumber of molelcules
Total (without water)331,55424
Polymers326,7988
Non-polymers4,75716
Water0
1
B: N-methyltransferase CkTcS
hetero molecules

C: N-methyltransferase CkTcS
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,8896
Polymers81,6992
Non-polymers1,1894
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_455x-1,y,z1
Buried area1960 Å2
ΔGint-8 kcal/mol
Surface area25930 Å2
MethodPISA
2
A: N-methyltransferase CkTcS
D: N-methyltransferase CkTcS
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,8896
Polymers81,6992
Non-polymers1,1894
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2070 Å2
ΔGint-11 kcal/mol
Surface area26340 Å2
MethodPISA
3
E: N-methyltransferase CkTcS
hetero molecules

G: N-methyltransferase CkTcS
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,8896
Polymers81,6992
Non-polymers1,1894
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_655x+1,y,z1
Buried area2000 Å2
ΔGint-12 kcal/mol
Surface area26700 Å2
MethodPISA
4
F: N-methyltransferase CkTcS
hetero molecules

H: N-methyltransferase CkTcS
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,8896
Polymers81,6992
Non-polymers1,1894
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_565x,y+1,z1
Buried area2060 Å2
ΔGint-9 kcal/mol
Surface area27480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.744, 86.812, 123.258
Angle α, β, γ (deg.)90.211, 90.039, 90.172
Int Tables number1
Space group name H-MP1
Space group name HallP1
Symmetry operation#1: x,y,z

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Components

#1: Protein
N-methyltransferase CkTcS


Mass: 40849.703 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Camellia sinensis var. assamica (Assam tea)
Production host: Escherichia coli (E. coli) / References: UniProt: Q9FZN8*PLUS
#2: Chemical
ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE / 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-EXU / 1,3,7-trimethyl-9H-purine-2,6,8-trione / 1,3,7-Trimethyluric acid


Mass: 210.190 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C8H10N4O3 / Comment: alkaloid*YM
Has ligand of interestY

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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: 2.93 Å3/Da / Density % sol: 57.97 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 0.1 M HEPES (pH 7.5), 1 M Sodium Citrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 1, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.14→50 Å / Num. obs: 62167 / % possible obs: 96.4 % / Redundancy: 2.5 % / Biso Wilson estimate: 62.383110248 Å2 / CC1/2: 0.995 / Net I/σ(I): 9.7
Reflection shellResolution: 3.15→3.2 Å / Rmerge(I) obs: 1.11 / Num. unique obs: 55414 / CC1/2: 0.845

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Processing

Software
NameVersionClassification
PHENIX1.9_1692+SVNrefinement
PHENIX1.9_1692+SVNrefinement
HKL-2000data scaling
PHENIXphasing
Cootmodel building
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2EFJ
Resolution: 3.15000316024→43.8717918208 Å / SU ML: 0.464226211064 / Cross valid method: THROUGHOUT / σ(F): 1.96340305611 / Phase error: 34.9015671293
RfactorNum. reflection% reflection
Rfree0.29805388409 2254 3.62571782457 %
Rwork0.262661324434 --
obs0.263952027126 62167 99.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 3.15000316024→43.8717918208 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms20792 0 0 0 20792
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0037338999945421222
X-RAY DIFFRACTIONf_angle_d0.83045017939728955
X-RAY DIFFRACTIONf_chiral_restr0.02963655526823425
X-RAY DIFFRACTIONf_plane_restr0.003798740337253693
X-RAY DIFFRACTIONf_dihedral_angle_d15.77255123097073
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.15001-3.21850.434939878595810.3394737764562267X-RAY DIFFRACTION29.8499872871
3.2185-3.29330.378919087478740.3129396093972524X-RAY DIFFRACTION33.1800766284
3.2933-3.37560.332452976916920.3079483911042786X-RAY DIFFRACTION36.6064614602
3.3756-3.46690.3427083649621180.290993500242983X-RAY DIFFRACTION39.8483680288
3.4669-3.56890.3636038804431310.3003930373713334X-RAY DIFFRACTION43.9386254121
3.5689-3.6840.3248480313041440.2860439391743618X-RAY DIFFRACTION47.6202531646
3.684-3.81560.2804095121021280.276790270273613X-RAY DIFFRACTION47.8266428024
3.8156-3.96830.3095526566751360.2674941485693682X-RAY DIFFRACTION47.6416271525
3.9683-4.14870.2566726397111363488X-RAY DIFFRACTION46.6409266409
4.1487-4.36730.2808492953211280.2454596611223535X-RAY DIFFRACTION46.3436234818
4.3673-4.64060.2860130296761440.2387155503073501X-RAY DIFFRACTION46.8268242549
4.6406-4.99850.3052119785841570.2326443012633837X-RAY DIFFRACTION50.6082108464
4.9985-5.50060.2770848490561630.2504297325694480X-RAY DIFFRACTION59.011184545
5.5006-6.29460.3240488424322200.2578868271125253X-RAY DIFFRACTION69.3135764944
6.2946-7.92290.2728174156122400.2686822089585970X-RAY DIFFRACTION79.0478615071
7.9229-43.80.278471370891620.246551836755042X-RAY DIFFRACTION66.4623243934
Refinement TLS params.

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

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
11.9429-0.6121-1.33552.991-1.97762.9660.008-0.2020.03720.1966-0.2579-0.1479-0.12010.10170.08551.16260.13740.12551.2676-0.02960.697215.147-17.8123-58.2511
24.4868-0.60681.50293.4825-0.82684.76970.0157-0.88240.36310.2680.8448-0.16780.36850.1663-0.41381.06640.34290.00791.0973-0.16460.81278.8316-24.3848-50.2421
31.66811.1887-0.34543.319-1.10361.1693-0.0461-0.38260.22620.23480.0618-0.0590.26250.3464-0.09320.8570.1201-0.02330.9547-0.06610.79111.9989-5.2829-54.2246
43.28350.23910.35333.2461-0.96062.345-0.05550.8230.1947-0.5954-0.3362-0.48420.93660.5269-0.03440.96720.22810.07041.1706-0.07880.676819.739-4.9104-66.5841
50.88810.9884-0.1755.1220.68150.2341-0.53080.0392-0.2982-1.32580.0814-0.48810.02960.4677-0.39171.03380.09720.01431.4470.13240.441275.2966-26.2412-69.0976
63.7469-0.66680.09564.70820.63542.7363-1.0595-0.61010.29520.09980.6267-0.220.4919-0.0085-0.50920.77830.2020.13611.60730.26430.225563.6579-20.6803-49.6341
74.7329-1.3534-1.56133.35121.61991.17990.4053-0.37760.1071-0.30620.8366-0.17830.08490.35880.14751.0870.1509-0.10161.3206-0.23810.08975.6226-20.5079-46.7382
81.99360.35470.31681.7986-0.8480.55990.1788-0.6190.2218-0.36390.51040.79380.3067-0.1735-0.10461.0404-0.17050.15451.14-0.26861.066969.5222-12.8296-47.4135
91.66671.340.22523.41071.51740.5569-0.153-0.1976-0.3558-0.20210.1546-0.40490.0433-0.087-0.13280.94710.11690.00830.94980.10610.573474.1431-34.1149-55.2406
102.96040.90221.25593.07890.21760.5666-0.8819-0.2277-0.335-0.15510.4715-0.094-0.13021.1206-0.15051.15230.0483-0.02621.1776-0.0660.639266.0861-42.5034-71.9828
113.1655-0.37412.0693.4756-0.0463.8059-0.5094-0.2784-0.10170.00130.40810.2519-0.2174-0.51860.15371.10810.00140.00931.15160.04260.596360.741-33.9385-53.0653
122.20430.9110.58132.53981.43910.741-0.51570.76160.1599-0.90430.37610.00460.14020.39550.05321.2012-0.06790.0041.0370.10870.469764.8878-32.5536-71.3482
132.3639-0.53421.24712.55071.83633.6751-0.3015-0.2150.4063-0.1921-0.12180.3587-0.3556-0.19540.29670.27140.0199-0.05490.23770.04610.622210.0703-56.1273-119.563
143.8691-0.45-1.16782.89690.64753.20590.0339-0.5668-0.12840.27780.20970.2002-0.32550.0945-0.13270.19170.12940.03060.19920.04050.539517.7671-48.7388-112.3893
151.83780.27860.12222.83250.48872.63410.01970.0476-0.4142-0.05920.20380.43010.1905-0.54-0.15380.134-0.0411-0.01970.31680.13250.53278.7202-70.2679-123.6239
162.33640.8103-0.69453.06181.22252.87170.06510.15950.0644-0.1151-0.18570.615-0.0919-0.2819-0.00480.2935-0.02130.09780.16260.10050.81453.6162-7.2903-128.3184
173.39280.71740.16444.03380.69722.90370.28760.456-0.0067-0.58690.0880.4924-0.1562-0.5794-0.00750.137-0.1727-0.0381-0.00670.05650.652260.7704-13.4008-136.4311
182.5381-0.8205-0.32742.31770.80821.3284-0.05250.08660.5347-0.12240.17570.4552-0.1281-0.3358-0.06510.2568-0.0153-0.05220.23820.13320.675656.02636.1161-128.9914
191.4758-0.4074-0.36592.2728-0.13115.7312-0.18990.4347-0.19280.3550.56840.0024-0.3399-0.28020.43380.19830.09540.1511-0.08240.04650.963354.614513.7019-117.3125
202.3117-0.2685-1.01232.4302-0.30134.2804-0.16950.32430.1269-0.31870.05810.3703-0.2022-0.9082-0.05230.3385-0.0353-0.17370.58170.17680.71645.95443.3354-134.125
216.73941.2571.07793.12040.98162.5297-0.3973-0.67720.29960.77480.28130.9073-0.0015-0.0424-0.12540.2019-0.00090.13660.2131-0.01690.661152.55650.495-111.9553
222.7336-0.333-0.50772.10151.03693.5991-0.2076-0.49540.13660.16090.01270.4187-0.0795-0.27460.01350.27280.0397-0.00870.22820.0420.583748.96682.8739-117.9752
234.66982.21390.79917.7486-0.04280.7355-0.2357-1.5720.52931.2002-0.1724-0.33180.3866-0.74370.14931.17460.1154-0.17631.463-0.01740.586952.890917.2105-56.0954
247.1381-0.3141-0.17417.1283-0.82340.9279-1.1795-0.12770.2639-1.6794-0.4748-0.0843-0.01890.44870.19121.6038-0.01420.24060.6558-0.22491.199864.175522.7172-76.4094
256.64532.3322-2.64346.7781-2.49215.8870.2472-0.52390.3022-0.6106-0.5633-0.5323-0.03431.62560.00531.01470.20840.09250.9784-0.06780.758355.520526.7301-77.445
265.34581.1735-1.86354.6412-2.27545.81070.0066-0.2529-0.0019-0.08080.34590.46160.29550.6604-0.21910.89070.061-0.06970.8961-0.07050.598947.907826.7838-71.2151
273.0806-0.2215-0.02252.7385-0.67241.3536-0.41650.4505-0.3321-0.20080.5271-0.529-0.1959-0.1733-0.19671.06750.1748-0.00630.7629-0.12490.93854.52013.044-67.0649
282.95560.49660.39443.6847-1.84612.2301-0.10950.272-0.9459-0.1686-0.1721-0.31540.1269-0.5245-0.10851.06180.35050.03651.2022-0.05150.88760.25564.4201-70.0753
292.6753-0.5171-3.75812.85230.785.2682-0.2199-1.6635-1.16621.50220.0664-0.3205-0.3282-0.5844-0.19871.06290.199-0.25641.31630.21530.586959.2731-2.1113-43.5997
303.5419-0.25590.50493.2794-0.58741.6965-0.14920.213-0.00660.25950.3936-0.8202-0.0039-0.0002-0.02661.04350.24550.01920.8097-0.13291.106563.74579.315-63.251
312.8537-0.82190.48582.4722-0.57488.7276-0.1087-0.15940.31850.6773-0.00740.0704-0.25170.6484-0.52381.47080.3679-0.02541.1020.01350.354165.314310.1259-55.9117
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'B' and (resid 9 through 51 )B9 - 51
2X-RAY DIFFRACTION2chain 'B' and (resid 52 through 119 )B52 - 119
3X-RAY DIFFRACTION3chain 'B' and (resid 120 through 235 )B120 - 235
4X-RAY DIFFRACTION4chain 'B' and (resid 236 through 369 )B236 - 369
5X-RAY DIFFRACTION5chain 'C' and (resid 9 through 28 )C9 - 28
6X-RAY DIFFRACTION6chain 'C' and (resid 29 through 51 )C29 - 51
7X-RAY DIFFRACTION7chain 'C' and (resid 52 through 71 )C52 - 71
8X-RAY DIFFRACTION8chain 'C' and (resid 72 through 91 )C72 - 91
9X-RAY DIFFRACTION9chain 'C' and (resid 92 through 235 )C92 - 235
10X-RAY DIFFRACTION10chain 'C' and (resid 236 through 275 )C236 - 275
11X-RAY DIFFRACTION11chain 'C' and (resid 276 through 307 )C276 - 307
12X-RAY DIFFRACTION12chain 'C' and (resid 308 through 369 )C308 - 369
13X-RAY DIFFRACTION13chain 'D' and (resid 9 through 52 )D9 - 52
14X-RAY DIFFRACTION14chain 'D' and (resid 53 through 137 )D53 - 137
15X-RAY DIFFRACTION15chain 'D' and (resid 138 through 369 )D138 - 369
16X-RAY DIFFRACTION16chain 'E' and (resid 9 through 51 )E9 - 51
17X-RAY DIFFRACTION17chain 'E' and (resid 52 through 117 )E52 - 117
18X-RAY DIFFRACTION18chain 'E' and (resid 118 through 255 )E118 - 255
19X-RAY DIFFRACTION19chain 'E' and (resid 256 through 275 )E256 - 275
20X-RAY DIFFRACTION20chain 'E' and (resid 276 through 307 )E276 - 307
21X-RAY DIFFRACTION21chain 'E' and (resid 308 through 331 )E308 - 331
22X-RAY DIFFRACTION22chain 'E' and (resid 332 through 369 )E332 - 369
23X-RAY DIFFRACTION23chain 'F' and (resid 9 through 28 )F9 - 28
24X-RAY DIFFRACTION24chain 'F' and (resid 29 through 52 )F29 - 52
25X-RAY DIFFRACTION25chain 'F' and (resid 53 through 90 )F53 - 90
26X-RAY DIFFRACTION26chain 'F' and (resid 91 through 137 )F91 - 137
27X-RAY DIFFRACTION27chain 'F' and (resid 138 through 192 )F138 - 192
28X-RAY DIFFRACTION28chain 'F' and (resid 193 through 245 )F193 - 245
29X-RAY DIFFRACTION29chain 'F' and (resid 246 through 264 )F246 - 264
30X-RAY DIFFRACTION30chain 'F' and (resid 265 through 331 )F265 - 331
31X-RAY DIFFRACTION31chain 'F' and (resid 332 through 369 )F332 - 369

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Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

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