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- PDB-8z8r: norbelladine 4'-O-methyltransferase S52T complexed with Mg and SAH -

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Basic information

Entry
Database: PDB / ID: 8z8r
Titlenorbelladine 4'-O-methyltransferase S52T complexed with Mg and SAH
ComponentsNorbelladine 4'-O-methyltransferase
KeywordsTRANSFERASE / O-methyltransferase family protein / NpN4OMT
Function / homology
Function and homology information


norbelladine O-methyltransferase / alkaloid metabolic process / S-adenosylmethionine-dependent methyltransferase activity / O-methyltransferase activity / methylation / metal ion binding
Similarity search - Function
: / O-methyltransferase / Class I-like SAM-dependent O-methyltransferase / SAM-dependent O-methyltransferase class I-type profile. / S-adenosyl-L-methionine-dependent methyltransferase superfamily
Similarity search - Domain/homology
S-ADENOSYL-L-HOMOCYSTEINE / Norbelladine 4'-O-methyltransferase
Similarity search - Component
Biological speciesNarcissus pseudonarcissus MK-2014 (plant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.79 Å
AuthorsSaw, Y.Y.H. / Nakashima, Y. / Morita, H.
Funding support Japan, 2items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)JP22H02777 Japan
Japan Society for the Promotion of Science (JSPS)JP22K15303 Japan
CitationJournal: Acs Catalysis / Year: 2024
Title: Structure-Based Catalytic Mechanism of Amaryllidaceae O-Methyltransferases
Authors: Hnin, S.Y.Y. / Nakashima, Y. / Kodama, T. / Morita, H.
History
DepositionApr 22, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 7, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Norbelladine 4'-O-methyltransferase
B: Norbelladine 4'-O-methyltransferase
C: Norbelladine 4'-O-methyltransferase
D: Norbelladine 4'-O-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)111,46314
Polymers109,6444
Non-polymers1,81910
Water18,1231006
1
A: Norbelladine 4'-O-methyltransferase
hetero molecules

D: Norbelladine 4'-O-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,7327
Polymers54,8222
Non-polymers9105
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y+1/2,-z+11
Buried area4500 Å2
ΔGint-44 kcal/mol
Surface area18300 Å2
MethodPISA
2
B: Norbelladine 4'-O-methyltransferase
C: Norbelladine 4'-O-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,7327
Polymers54,8222
Non-polymers9105
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4510 Å2
ΔGint-43 kcal/mol
Surface area18190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.352, 79.723, 91.517
Angle α, β, γ (deg.)90.000, 94.010, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein
Norbelladine 4'-O-methyltransferase / NpN4OMT


Mass: 27411.109 Da / Num. of mol.: 4 / Mutation: S52T
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Narcissus pseudonarcissus MK-2014 (plant)
Gene: N4OMT / Production host: Escherichia coli M15 (bacteria)
References: UniProt: A0A077EWA5, norbelladine O-methyltransferase
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE


Type: L-peptide linking / Mass: 384.411 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C14H20N6O5S / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1006 / Source method: isolated from a natural source / Formula: H2O
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: 2.14 Å3/Da / Density % sol: 42.41 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 25% (w/v) PEG 8000, 0.2M MgCl2, 0.1M Tris-HCl (pH 8.0)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-1A / Wavelength: 1.035 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Mar 4, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.035 Å / Relative weight: 1
ReflectionResolution: 1.79→45.65 Å / Num. obs: 86494 / % possible obs: 99.5 % / Redundancy: 4.3 % / Biso Wilson estimate: 16.89 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.101 / Net I/σ(I): 10.8
Reflection shellResolution: 1.79→1.82 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.658 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 4513 / CC1/2: 0.65 / % possible all: 98.3

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.79→45.65 Å / SU ML: 0.1798 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 18.2613
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1887 2000 2.31 %
Rwork0.1578 84475 -
obs0.1585 86475 99.45 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 20.88 Å2
Refinement stepCycle: LAST / Resolution: 1.79→45.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7776 0 12 1006 8794
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00448169
X-RAY DIFFRACTIONf_angle_d0.774511146
X-RAY DIFFRACTIONf_chiral_restr0.05021249
X-RAY DIFFRACTIONf_plane_restr0.00431434
X-RAY DIFFRACTIONf_dihedral_angle_d20.54843028
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.79-1.830.28861310.24685979X-RAY DIFFRACTION98.5
1.83-1.880.25311650.21685917X-RAY DIFFRACTION98.91
1.88-1.940.23731310.19026001X-RAY DIFFRACTION99.03
1.94-20.22161300.17966017X-RAY DIFFRACTION99.23
2-2.070.24051530.1786005X-RAY DIFFRACTION99.52
2.07-2.160.21811360.16955995X-RAY DIFFRACTION99.32
2.16-2.260.20781430.16036008X-RAY DIFFRACTION99.72
2.26-2.370.19611430.15686053X-RAY DIFFRACTION99.65
2.37-2.520.20921480.15896034X-RAY DIFFRACTION99.73
2.52-2.720.20731390.15636047X-RAY DIFFRACTION99.9
2.72-2.990.18041440.16146066X-RAY DIFFRACTION99.73
2.99-3.420.16951480.14496067X-RAY DIFFRACTION99.65
3.42-4.310.13471400.12416113X-RAY DIFFRACTION99.87
4.31-45.650.16121490.1486173X-RAY DIFFRACTION99.54
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)
10.01154200854510.0382664504403-0.001568965310270.1292600242550.04204261281860.0435859951923-0.0299239060756-0.177278804943-0.337296779130.1666730817790.0844114547049-0.1845005893950.1036098115620.2459989248367.25883487615E-50.206927324401-0.00421682425678-0.0384095544550.252462867772-0.0344119957290.33504525028910.81505850062.1932845875446.3985097349
20.0655586461115-0.0150450220021-0.03050551256170.023196964483-0.07457965382280.00259355815393-0.0471684834863-0.1271724751730.03822316171930.143753781867-0.02631963204-0.0161768759479-0.0181297335654-0.0331079940843-0.0001449313402650.1070625615320.0145386952848-0.01338783164740.124814568718-0.004954738057070.100406240659-4.94655938168-10.241364229450.8750359572
30.315285991517-0.0799235440472-0.01175220851410.0768463608458-0.08552923365870.208919672068-0.0142767171147-0.3828286206430.30337268398-0.07900331906370.156383994290.03398597956560.05471316677060.06613696971980.07285885487590.0942671888620.0166865559065-0.006871086117810.166274376167-0.05658622318010.1154456988269.62429489066-11.187521630552.836716914
40.06556101296520.0191735343367-0.002978283867870.0288188794712-0.01831791347830.0215214082965-0.03917665558780.0438273724498-0.05967001656-0.001022413596810.0415291634926-0.0497028472231-0.05178176114740.00717315572521-2.03683578019E-60.0941842432155-0.0088598323340.004368601639920.0874016508927-0.005660106909510.1102985922783.88069489593-20.305113226637.3170693603
50.1905156986560.0656969775685-0.07760853120670.1164108128970.04611081519540.120815161148-0.0906536416849-0.118171909482-0.03738150859260.009041896190770.0419049954493-0.0773428678063-0.00162124295620.0391240016542-0.05374630475220.08801584087340.0165861478642-0.0144620068570.1021725117660.004812370319790.097107759554113.968790388-20.620139209546.129088878
60.426863511159-0.1160444020770.0354063970140.1017324389330.02582251382160.0674142710273-0.0160507631840.146295399496-0.0266742118809-0.0103320556327-0.00588300566522-0.06796538395980.03347166859560.102892653030.009995121135620.066052122072-0.009663540947230.01251742065510.1103225175690.005203834444930.10368262950917.8689912855-18.349140867832.3023548944
70.336573941922-0.07003749844330.09645030429650.0657787413820.0006515681045170.075624645239-0.03545021677050.04034447405720.090953449453-0.03752250217180.110712178709-0.172989273702-0.05429188205480.1191120094940.01107558187240.0955586480277-0.02488726953960.004553861364780.0661836581558-0.01737709684370.1230279900028.7332692711-2.7320978796333.9536020139
80.217988798873-0.00597115568526-0.06135346630570.0390753229388-0.03358158327650.03948093954390.1179377265390.1164275526810.256178919902-0.0614626331492-0.0223915928999-0.173001066641-0.1224525157140.04541047178270.01898999190610.115079443891-0.0167932661520.02015898054710.08863687403380.004939997962540.15723014576612.42069524311.2871325520330.6627665568
90.056694389636-0.1264544360840.02423593007910.0655844667258-0.1412754548070.149272674568-0.05608336382630.09031077644620.04243291923460.0156262643644-0.0491260955766-0.02353525767930.0305968788756-0.016354524859-0.06191998005440.106667059808-0.01541835312840.002569697364070.118553150285-0.006978585545730.06696911724854.46872481472-11.107658738126.6045297557
100.08423430390440.04125932369530.03658076898910.338799029069-0.092520293589-0.020374942778-0.06301417595420.01576137819740.02639132034770.07940382349470.023362699413-0.240357071609-0.07147166782310.0364306212536-0.007378520536480.1158918429020.005354025965580.0136811206430.105061306509-0.001115115590280.14369089108532.7838667481-7.7836091661489.1265805058
110.207807967922-0.0299985155152-0.1950062274090.173436478107-0.1769612474870.305673014195-0.0645953253519-0.0283420196014-0.00531072229064-0.002614325265220.0655055637549-0.0303104640966-0.03693483642250.002257801710760.009388176142590.11530082938-0.001429738690150.006901287675690.0793877783771-0.01558663100740.092460993803633.5721088972-19.809272564584.1237440055
120.661700398599-0.0888399286212-0.3680958031610.2586837054480.08921833869460.3183676374-0.0397273284180.205486448824-0.10631553802-0.09618827994840.0695570940368-0.1597986122630.1329647837970.006159340833190.02499031924920.154893687447-0.03131050277360.01989303852070.129164024232-0.03115163357390.12045813802135.4536962483-23.315254611671.5052387102
130.307464709217-0.149554223966-0.08926635010420.1493786794850.05059295143240.255022743371-0.004076099937220.1189213109130.0845457385766-0.05351820269650.02827656846410.00500805337813-0.0329086196801-0.0554656089180.04403387208320.131109148503-0.0264304436678-0.005123085348510.1064671219980.01210818332610.07474837094424.814334723-8.0292597824172.5426072528
140.6785594591590.194324227906-0.1035185752820.190878970215-0.2083315406370.369220508623-0.002281102422220.08970341488720.1102387685180.007771858545660.0475981096760.0630298530806-0.069380597061-0.1154046242290.01917900403870.1054022372590.00833509338964-0.007896795912530.1317099040820.0240326844380.1116418243243.22188735374-10.724942944883.7859202682
150.175486708356-0.01284380964750.004305151088290.159226458891-0.1612583888670.100245139622-0.0233259189481-0.08619297986-0.117773000456-0.02543669859260.1246220103550.1055602472470.0459822380068-0.1241190631550.01025938213980.143559294987-0.01385987954830.01429401887860.1408856275210.03611949640460.1386177541053.65694153312-26.261609433394.7188595017
160.2234235560580.187637827397-0.1328368867320.131890494305-0.06723955418370.1816819787350.01118362888720.009992984472130.01285199755590.009627910956240.02521435291830.02500854323330.00266748199107-0.0238228798010.02395889469510.1281118642910.01330171936640.002139779526570.0700401519940.01264054873670.083091456742714.7757702968-15.799351325197.3766982515
170.0120481486210.0186484228357-0.03253321421150.0228426360385-0.07023842770520.0753501597050.0401770201430.02985553705710.09728100700270.04103062822870.00906912557031-0.08334818132550.002732973105970.1538778091761.87321791769E-50.1990730378640.013080218584-0.01667122210250.203316575024-0.008864200843580.21455953729512.7073141533-36.846091597553.7975919264
180.0261117114311-0.0612418690732-0.01749098775440.0296997514512-0.001562942559780.04868933389390.0651312950399-0.2221597608550.125682284838-0.0269700305075-0.03427050608820.0557005955361-0.08633302820490.13897533934-2.18091075131E-50.1425620617990.00264649402222-0.01177771395760.156099152514-0.02966804604660.136596946967-3.70580963481-39.014322139265.058581641
190.18271470948-0.16880342706-0.04485442242640.1893500235-0.007192761704070.020487572339-0.0505344317569-0.1915846149790.488349353144-0.02680566215590.076019734124-0.159145038493-0.072767721318-0.0422769172521-0.008466155904290.139038499340.00675891204063-0.008670750632220.202348310755-0.06942041551410.17157763366810.85993136-40.588420168768.2469731528
200.08063687563390.0186061676631-0.08934426792360.03921414308510.008536334363210.0413341153325-0.0839213022506-0.199302926052-0.0625857089079-0.0326610636880.104367637753-0.0612871041495-0.00644758527811-0.0264940096853-0.00653816492620.09044907496830.00654305749245-0.004639324399150.1455289959280.01800930595190.1151891716882.04070456758-57.306802003264.0506507588
210.1505757892750.079290408182-0.1197065548280.1849824224390.01144388170830.138121061376-0.224030258736-0.364644402567-0.0194299692580.05994556418680.163754018821-0.09542090338490.08913178179340.129347165598-0.03272776290710.1039383365970.0376701772305-0.0365014914420.23927016211-0.00982023991040.10355273259312.7274418448-52.726756666570.9992316
220.109608658760.1084543847560.0256897109690.6259443004750.1606021092130.215935678225-0.106649073928-0.295263210154-0.456851079484-0.2437203720890.258243174397-0.653968904252-0.1075352834350.1813641878390.0440070716710.02898281719090.0718501492739-0.1045219621280.2328203087050.0970797968450.11995382000218.8874802254-61.940818772165.5450457778
230.135240049483-0.09751870650090.02669530220390.0662433445125-0.02809225899960.0336726796066-0.0119567682056-0.0688306817388-0.1010159496430.08066498122360.0483667429926-0.02650991164890.08511661738490.1762252644260.03205519353280.08413236775750.01652782259290.001258515218190.1296317418960.005456113917040.14542062765513.5169624052-62.535489232256.5269050515
240.363569733726-0.1481311306820.09908762832050.129564061226-0.0679895020193-0.0282688430147-0.09109622566190.01795858910520.119546613208-0.01293489825510.131700908674-0.0320338103783-0.00263781808938-0.01022319816850.009393678662770.0937307741898-0.02349193687730.0008032130055680.065944744557-0.003593266158680.1390937920549.80892325809-48.217946647248.8238201584
250.028514184472-0.03828989263320.08668767763150.0483028620678-0.03377607729030.0297565648425-0.120954344340.0689731813595-0.0620709192442-0.1177937065070.0959940499869-0.175236668356-0.02154807290070.0208557392556-1.63386606234E-50.104640933305-0.006523729220410.009301144030390.0875032476865-0.00203638706660.11173648957113.8517158772-49.31377395844.3502043504
260.0839425769757-0.1196780630880.07651278736510.0520914496156-0.05097515359020.12660573272-0.032835530365-0.00057973918186-0.06200846436720.0151761149750.0293926314866-0.00540545606825-0.02391440272690.0349677454952-0.009973008198430.0869220283898-0.008610488685030.01462553634720.0699858317385-0.01505486294170.106833377623.48236087501-58.928761466149.9825920937
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid -2 through 18 )
2X-RAY DIFFRACTION2chain 'A' and (resid 19 through 35 )
3X-RAY DIFFRACTION3chain 'A' and (resid 36 through 56 )
4X-RAY DIFFRACTION4chain 'A' and (resid 57 through 78 )
5X-RAY DIFFRACTION5chain 'A' and (resid 79 through 119 )
6X-RAY DIFFRACTION6chain 'A' and (resid 120 through 171 )
7X-RAY DIFFRACTION7chain 'A' and (resid 172 through 198 )
8X-RAY DIFFRACTION8chain 'A' and (resid 199 through 217 )
9X-RAY DIFFRACTION9chain 'A' and (resid 218 through 239 )
10X-RAY DIFFRACTION10chain 'B' and (resid -2 through 35 )
11X-RAY DIFFRACTION11chain 'B' and (resid 36 through 92 )
12X-RAY DIFFRACTION12chain 'B' and (resid 93 through 171 )
13X-RAY DIFFRACTION13chain 'B' and (resid 172 through 239 )
14X-RAY DIFFRACTION14chain 'C' and (resid -2 through 131 )
15X-RAY DIFFRACTION15chain 'C' and (resid 132 through 171 )
16X-RAY DIFFRACTION16chain 'C' and (resid 172 through 239 )
17X-RAY DIFFRACTION17chain 'D' and (resid -2 through 18 )
18X-RAY DIFFRACTION18chain 'D' and (resid 19 through 35 )
19X-RAY DIFFRACTION19chain 'D' and (resid 36 through 56 )
20X-RAY DIFFRACTION20chain 'D' and (resid 57 through 78 )
21X-RAY DIFFRACTION21chain 'D' and (resid 79 through 119 )
22X-RAY DIFFRACTION22chain 'D' and (resid 120 through 142 )
23X-RAY DIFFRACTION23chain 'D' and (resid 143 through 171 )
24X-RAY DIFFRACTION24chain 'D' and (resid 172 through 198 )
25X-RAY DIFFRACTION25chain 'D' and (resid 199 through 217 )
26X-RAY DIFFRACTION26chain 'D' and (resid 218 through 239 )

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