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- PDB-4e70: Crystal Structure Analysis of Coniferyl Alcohol 9-O-Methyltransfe... -

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Basic information

Entry
Database: PDB / ID: 4.0E+70
TitleCrystal Structure Analysis of Coniferyl Alcohol 9-O-Methyltransferase from Linum Nodiflorum in Complex with Coniferyl Alcohol
ComponentsConiferyl alcohol 9-O-methyltransferase
KeywordsTRANSFERASE / S-Adenosyl-L-methionine / small molecule O-methyltransferase / coniferyl alcohol / Dimer / Rossmann fold
Function / homology
Function and homology information


acetylserotonin O-methyltransferase activity / melatonin biosynthetic process / methylation / protein dimerization activity
Similarity search - Function
Plant methyltransferase dimerisation / Dimerisation domain / O-methyltransferase domain / O-methyltransferase domain / SAM-dependent O-methyltransferase class II-type profile. / O-methyltransferase COMT-type / Vaccinia Virus protein VP39 / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A / Winged helix DNA-binding domain superfamily ...Plant methyltransferase dimerisation / Dimerisation domain / O-methyltransferase domain / O-methyltransferase domain / SAM-dependent O-methyltransferase class II-type profile. / O-methyltransferase COMT-type / Vaccinia Virus protein VP39 / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
4-[(1E)-3-hydroxyprop-1-en-1-yl]-2-methoxyphenol / Coniferyl alcohol 9-O-methyltransferase
Similarity search - Component
Biological speciesLinum nodiflorum (plant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6093 Å
AuthorsWolters, S. / Heine, A. / Petersen, M.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2013
Title: Structural analysis of coniferyl alcohol 9-O-methyltransferase from Linum nodiflorum reveals a novel active-site environment.
Authors: Wolters, S. / Neeb, M. / Berim, A. / Schulze Wischeler, J. / Petersen, M. / Heine, A.
History
DepositionMar 16, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 1, 2013Provider: repository / Type: Initial release
Revision 1.1May 15, 2013Group: Database references
Revision 1.2Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Coniferyl alcohol 9-O-methyltransferase
B: Coniferyl alcohol 9-O-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,4887
Polymers86,8512
Non-polymers6375
Water11,998666
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10660 Å2
ΔGint-74 kcal/mol
Surface area27700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.018, 104.451, 109.800
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Coniferyl alcohol 9-O-methyltransferase / S-adenosyl-L-methionine-dependent coniferyl alcohol 9-O-methyltransferase


Mass: 43425.492 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Linum nodiflorum (plant) / Gene: CA9OMT / Plasmid: pet15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: A6XNE6
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-N7I / 4-[(1E)-3-hydroxyprop-1-en-1-yl]-2-methoxyphenol / Coniferyl alcohol


Mass: 180.200 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H12O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 666 / 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: 2.5 Å3/Da / Density % sol: 50.77 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 1 M Na/K phosphate, 0.7M ammonium sulfate, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.91841 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 8, 2011 / Details: Mirror
RadiationMonochromator: Double Crystal Monochromator Si-111 crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91841 Å / Relative weight: 1
ReflectionResolution: 1.609→30 Å / Num. all: 111552 / Num. obs: 111552 / % possible obs: 98.1 % / Redundancy: 5.2 % / Rsym value: 0.04 / Χ2: 1.002 / Net I/σ(I): 19
Reflection shell
Resolution (Å)Redundancy (%)Num. unique allRsym valueΧ2Diffraction-ID% possible all
1.609-1.644.151290.4570.939191.6
1.64-1.674.152580.3990.921193.5
1.67-1.74.152830.3490.983194.1
1.7-1.734.354230.2860.911196
1.73-1.774.454250.2340.923196.7
1.77-1.814.554750.20.928197.8
1.81-1.864.755880.1690.963198.8
1.86-1.914.855490.1410.995198.8
1.91-1.96556410.1130.996199.5
1.96-2.035.356080.0940.996199.8
2.03-2.15.456440.081.036199.8
2.1-2.185.756520.0711.004199.9
2.18-2.285.856680.0751.047199.9
2.28-2.4656770.0741.0451100
2.4-2.56657050.071.0461100
2.56-2.756.157020.0641.044199.9
2.75-3.036.157250.051.0461100
3.03-3.476.157500.0291.0121100
3.47-4.37657810.0191.029199.7
4.37-305.858690.0161.008197.1

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
PHENIX1.7.2_869refinement
PDB_EXTRACT3.1data extraction
MAR345dtbdata collection
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.6093→23.256 Å / Occupancy max: 1 / Occupancy min: 0.21 / FOM work R set: 0.8801 / SU ML: 0.4 / σ(F): 1.34 / Phase error: 18.8 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1914 5566 5 %RANDOM
Rwork0.17 ---
obs0.1711 105779 97.98 %-
all-111345 --
Solvent computationShrinkage radii: 1.11 Å / VDW probe radii: 1.3 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 41.419 Å2 / ksol: 0.375 e/Å3
Displacement parametersBiso max: 80.6 Å2 / Biso mean: 24.8352 Å2 / Biso min: 9.76 Å2
Baniso -1Baniso -2Baniso -3
1-0.266 Å20 Å2-0 Å2
2--1.7348 Å20 Å2
3----2.0008 Å2
Refinement stepCycle: LAST / Resolution: 1.6093→23.256 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5525 0 44 666 6235
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0065818
X-RAY DIFFRACTIONf_angle_d1.0437928
X-RAY DIFFRACTIONf_chiral_restr0.071884
X-RAY DIFFRACTIONf_plane_restr0.0051016
X-RAY DIFFRACTIONf_dihedral_angle_d12.7192075
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.6093-1.62760.24411590.23013170332989
1.6276-1.64680.27271630.22243329349293
1.6468-1.66680.24371920.21593281347393
1.6668-1.68790.26121660.22033395356194
1.6879-1.71010.27141710.20263356352795
1.7101-1.73360.20861870.19183436362396
1.7336-1.75830.19741770.18373439361697
1.7583-1.78450.21091730.17863458363197
1.7845-1.81240.20251920.17663469366198
1.8124-1.84210.21741840.183532371699
1.8421-1.87390.20991660.17583567373399
1.8739-1.90790.18451700.1613529369999
1.9079-1.94460.17051740.16163559373399
1.9446-1.98430.18711790.173235653744100
1.9843-2.02740.21371740.174235903764100
2.0274-2.07450.19931910.176635723763100
2.0745-2.12640.20082260.173435353761100
2.1264-2.18380.19561820.169235713753100
2.1838-2.24810.19821980.172635583756100
2.2481-2.32060.19791970.167735793776100
2.3206-2.40340.20311920.172435853777100
2.4034-2.49950.20722070.174635743781100
2.4995-2.61310.2041890.173236063795100
2.6131-2.75070.20491990.183235913790100
2.7507-2.92270.20432000.192136083808100
2.9227-3.14790.20981620.178236463808100
3.1479-3.46380.18332060.164536163822100
3.4638-3.96280.1592110.147936273838100
3.9628-4.98470.15331770.13433716389399
4.9847-23.25880.18212020.17863708391097
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)
11.253-0.5911-0.03561.43110.11560.6868-0.0292-0.0763-0.06610.25780.046-0.01370.0214-0.0086-0.03420.1611-0.009-0.00770.09060.02160.071610.1903-25.8937-19.3551
21.2701-0.23560.06692.31150.03450.97030.02470.14380.3112-0.0924-0.054-0.5424-0.23620.25170.04330.1737-0.04910.01670.19440.03650.187517.0321-8.9558-39.1382
31.2912-0.1817-0.36621.17160.10610.75430.01760.1445-0.0689-0.1235-0.0098-0.124-0.03970.01610.00130.05140.00090.01250.1117-0.00380.092112.0582-23.6174-54.7445
40.8267-1.2321-0.60527.94473.48752.4652-0.0863-0.0486-0.04450.34550.1523-0.01660.11390.104-0.06730.0906-0.00490.00220.12870.02720.1027.1872-21.5079-35.5611
52.8809-0.5935-0.76972.8175-0.59461.81920.01050.16820.0532-0.1318-0.02360.1934-0.2401-0.20210.00760.17510.028-0.00980.0870.00680.109-7.284-2.8606-39.4759
62.924-1.15650.08131.96790.09590.6845-0.0878-0.23070.32630.34550.1108-0.2355-0.23480.0582-0.02870.2756-0.0357-0.010.142-0.00520.142312.5493-6.6098-16.7019
76.05721.7497-2.13891.9459-0.85382.43210.175-0.03540.26530.21870.01240.0757-0.4117-0.0833-0.1830.31370.0380.04710.14710.00230.1869-4.7968-3.5887-12.5743
82.5306-1.27130.72533.1926-0.24993.6558-0.13060.07280.45640.24540.0265-0.1287-0.3686-0.11260.05480.25710.03440.06190.1670.02210.2028-10.6163-1.10330.1254
92.9288-0.2925-0.82081.49960.05092.11360.062-0.43220.25990.35670.0503-0.0171-0.04130.2662-0.09410.3004-0.01540.05780.20590.00260.1775-0.2033-13.39461.335
101.81090.0901-1.35060.4432-0.10011.95840.0221-0.2235-0.06970.1917-0.01710.05630.10390.0695-0.00350.20460.00390.03010.10950.0210.117-0.6441-19.9568-5.2502
113.8553-3.66381.21934.45351.19636.09450.4583-1.211-0.45681.0149-0.31031.34210.9274-1.3343-0.11390.3409-0.12790.00440.76790.10660.491330.3797-32.6034-43.4664
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resseq 1:107)A1 - 107
2X-RAY DIFFRACTION2chain 'A' and (resseq 108:168)A108 - 168
3X-RAY DIFFRACTION3chain 'A' and (resseq 169:368)A169 - 368
4X-RAY DIFFRACTION4chain 'B' and (resseq 1000:1034)B0
5X-RAY DIFFRACTION5chain 'B' and (resseq 1035:1107)B0
6X-RAY DIFFRACTION6chain 'B' and (resseq 1108:1168)B0
7X-RAY DIFFRACTION7chain 'B' and (resseq 1169:1193)B0
8X-RAY DIFFRACTION8chain 'B' and (resseq 1194:1250)B0
9X-RAY DIFFRACTION9chain 'B' and (resseq 1251:1312)B0
10X-RAY DIFFRACTION10chain 'B' and (resseq 1313:1368)B0
11X-RAY DIFFRACTION11chain 'B' and (resseq 993:996)B993 - 996

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