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

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Basic information

Entry
Database: PDB / ID: 4evi
TitleCrystal Structure Analysis of Coniferyl Alcohol 9-O-Methyltransferase from Linum Nodiflorum in Complex with Coniferyl Alcohol 9-Methyl Ether and S -Adenosyl-L-Homocysteine
ComponentsConiferyl alcohol 9-O-methyltransferase
KeywordsTRANSFERASE / Rossmann fold / Dimer / small molecule O-methyltransferase / S-Adenosyl-L-methionine / coniferyl alcohol / S -Adenosyl-L-homocysteine
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
2-methoxy-4-[(1E)-3-methoxyprop-1-en-1-yl]phenol / 4-[(1E)-3-hydroxyprop-1-en-1-yl]-2-methoxyphenol / S-ADENOSYL-L-HOMOCYSTEINE / Coniferyl alcohol 9-O-methyltransferase
Similarity search - Component
Biological speciesLinum nodiflorum (plant)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.015 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
DepositionApr 26, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 1, 2013Provider: repository / Type: Initial release
Revision 1.1May 15, 2013Group: Database references
Revision 1.2Sep 13, 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 / 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)87,9789
Polymers86,8512
Non-polymers1,1277
Water8,089449
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10640 Å2
ΔGint-71 kcal/mol
Surface area27230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.842, 105.042, 108.983
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 2 molecules AB

#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

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Non-polymers , 5 types, 456 molecules

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


Type: L-peptide linking / Mass: 384.411 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H20N6O5S
#3: Chemical ChemComp-C9M / 2-methoxy-4-[(1E)-3-methoxyprop-1-en-1-yl]phenol


Mass: 194.227 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H14O3
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 180.200 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H12O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 449 / 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: 50.78 %
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: SEALED TUBE / Type: OTHER / Wavelength: 1.54178 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Aug 8, 2011
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 2.015→10 Å / Num. all: 57450 / Num. obs: 57450 / % possible obs: 99.8 % / Redundancy: 5.2 % / Rsym value: 0.091 / Χ2: 1.039 / Net I/σ(I): 9.7
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.015-2.055.10.50228400.998199.9
2.05-2.095.10.42927991.043199.8
2.09-2.135.10.39528601.0251100
2.13-2.175.10.31628750.9971100
2.17-2.225.10.29528201.055199.8
2.22-2.275.10.27428151.055199.9
2.27-2.335.20.22828801.0351100
2.33-2.395.20.20728351.06199.9
2.39-2.465.20.18728741.048199.9
2.46-2.545.20.16828551.066199.9
2.54-2.635.20.14528551.0261100
2.63-2.735.20.12728631.0641100
2.73-2.855.30.11528681.0371100
2.85-35.20.10128481.051199.8
3-3.185.20.08329101.072199.9
3.18-3.425.30.06629011.0441100
3.42-3.745.30.05628901.0591100
3.74-4.255.30.05129401.0071100
4.25-5.225.20.04329511.0991100
5.22-104.60.04429710.919197.6

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 28.42 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.6 Å24.91 Å
Translation2.6 Å24.91 Å

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
PHASER2.1.4phasing
PHENIX1.7.1_743refinement
PDB_EXTRACT3.11data extraction
MAR345dtbdata collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4EMS
Resolution: 2.015→9.34 Å / Occupancy max: 1 / Occupancy min: 0.34 / FOM work R set: 0.8789 / SU ML: 0.48 / σ(F): 1.34 / Phase error: 19 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2031 2903 5.07 %RANDOM
Rwork0.1759 ---
obs0.1773 57246 99.5 %-
all-57246 --
Solvent computationShrinkage radii: 1.06 Å / VDW probe radii: 1.3 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 52.478 Å2 / ksol: 0.447 e/Å3
Displacement parametersBiso max: 71.43 Å2 / Biso mean: 25.3694 Å2 / Biso min: 8.56 Å2
Baniso -1Baniso -2Baniso -3
1--1.7907 Å20 Å20 Å2
2--1.6305 Å20 Å2
3---0.1602 Å2
Refinement stepCycle: LAST / Resolution: 2.015→9.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5515 0 77 449 6041
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0075855
X-RAY DIFFRACTIONf_angle_d1.017980
X-RAY DIFFRACTIONf_chiral_restr0.065887
X-RAY DIFFRACTIONf_plane_restr0.0051022
X-RAY DIFFRACTIONf_dihedral_angle_d13.512086
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 21

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.015-2.04770.2721270.22242428255595
2.0477-2.08270.24951480.205525352683100
2.0827-2.12010.24161330.199125912724100
2.1201-2.16040.25791180.181625892707100
2.1604-2.20390.22151380.180525552693100
2.2039-2.25120.24581380.179325772715100
2.2512-2.30280.21921460.168625752721100
2.3028-2.35950.19731430.166825632706100
2.3595-2.42220.21151340.164525842718100
2.4222-2.49220.22121400.160825812721100
2.4922-2.5710.18581560.156125582714100
2.571-2.66080.20811370.160625772714100
2.6608-2.76470.20351260.172526222748100
2.7647-2.8870.22041480.177725862734100
2.887-3.03420.20861380.174126082746100
3.0342-3.2170.21811320.178326052737100
3.217-3.45370.20111540.170226042758100
3.4537-3.78020.17991250.163526462771100
3.7802-4.28050.16981580.155726102768100
4.2805-5.23030.16911360.145226802816100
5.2303-9.340.20831280.26652669279797
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)
11.4720.6789-0.56460.8821-0.1121.33860.0231-0.0458-0.1031-0.0997-0.0205-0.1579-0.10780.1471-0.01970.21580.02180.0180.1707-0.02030.12140.0318-14.72521.9952
20.97350.48550.63871.6041-0.64432.9038-0.11680.01860.0201-0.48770.10020.15460.0686-0.19550.00110.2450.012-0.0320.1709-0.03790.1006-18.0007-30.568616.5614
30.93120.95450.67952.73390.56410.91920.1409-0.05770.0558-0.7519-0.27140.1789-0.197-0.1630.06090.07910.0314-0.00520.1402-0.03810.0442-14.0662-23.551529.8256
43.44660.5459-1.20382.1642-0.57152.44440.311-0.3845-0.12660.1379-0.46320.9795-0.329-0.7962-0.21440.10280.14270.11990.3068-0.21990.2653-17.0706-2.41244.275
50.93450.6282-0.26951.9373-0.64161.7328-0.03-0.0597-0.1486-0.03880.11110.08230.0315-0.1056-0.08480.0643-0.00890.00950.1668-0.03050.1108-16.1122-30.389451.0942
61.05310.0388-0.26751.20080.17750.75270.0643-0.16350.02070.1464-0.02890.2531-0.0667-0.1397-0.02450.09150.0060.0320.1972-0.01620.1191-20.4009-24.226557.7565
71.2748-0.5787-0.28222.51550.4542.60650.1227-0.37660.15040.27050.0668-0.0567-0.14090.1381-0.10130.0714-0.0446-0.00470.2259-0.04720.0819-5.3003-20.915159.4555
80.9625-0.15980.291.536-0.52261.26390.0234-0.10610.01850.0073-0.0167-0.178-0.06380.1136-0.00430.0616-0.01880.02640.1446-0.0210.0966-2.438-19.698351.8622
90.57170.47240.07181.5983-0.00050.5644-0.01940.0222-0.0116-0.21320.0093-0.1387-0.0237-0.0898-0.01040.12160.01230.01890.1789-0.02750.084-8.1572-22.101135.7895
103.26920.6602-0.69282.5481-0.01922.79340.0628-0.07280.167-0.0078-0.0906-0.211-0.31610.07280.0340.1583-0.02520.02570.09-0.01560.11045.3219-1.064740.2178
112.26740.44330.78211.17640.2630.9827-0.0720.04880.1085-0.20350.0445-0.0825-0.21750.00390.0330.19580.01080.050.0869-0.02570.09840.2355-6.594727.2152
123.68462.34660.24814.3646-0.28151.5132-0.22910.24760.6183-0.79870.21960.6313-0.1258-0.15130.0490.37620.0846-0.110.28090.01540.2466-19.8216-7.42411.4901
139.9872-3.1811-4.16262.95482.54673.07060.2284-0.01470.3388-0.1344-0.037-0.1154-0.36010.0889-0.25090.2937-0.03380.02240.17750.02010.15534.5543-3.678712.3998
143.33491.77671.13951.9676-1.68736.0124-0.1913-0.18080.1229-0.34450.0103-0.2779-0.18980.35480.18270.301-0.04820.09430.1943-0.02640.20412.3013-5.22230.0117
156.5854-0.4378-0.09864.4270.81253.8787-0.0244-0.2450.4348-0.6919-0.04930.1125-0.65790.10180.06940.33060.01460.00150.156-0.01220.20848.67492.3377-1.6547
161.69610.3205-0.71160.83750.02171.93260.00680.42070.1575-0.31370.0007-0.0488-0.0456-0.03680.05580.27310.00890.04620.20180.02230.102-1.0915-14.68742.2113
171.5247-0.0587-0.70650.47450.69193.03860.04940.2636-0.108-0.23690.0121-0.11980.1388-0.1115-0.04320.3366-0.01460.07030.189-0.01890.13812.7958-20.60790.191
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resseq 1:34)A1 - 34
2X-RAY DIFFRACTION2chain 'A' and (resseq 35:77)A35 - 77
3X-RAY DIFFRACTION3chain 'A' and (resseq 78:138)A78 - 138
4X-RAY DIFFRACTION4chain 'A' and (resseq 139:168)A139 - 168
5X-RAY DIFFRACTION5chain 'A' and (resseq 169:221)A169 - 221
6X-RAY DIFFRACTION6chain 'A' and (resseq 222:274)A222 - 274
7X-RAY DIFFRACTION7chain 'A' and (resseq 275:312)A275 - 312
8X-RAY DIFFRACTION8chain 'A' and (resseq 313:368)A313 - 368
9X-RAY DIFFRACTION9chain 'B' and (resseq -7:34)B-7 - 34
10X-RAY DIFFRACTION10chain 'B' and (resseq 35:77)B35 - 77
11X-RAY DIFFRACTION11chain 'B' and (resseq 78:138)B78 - 138
12X-RAY DIFFRACTION12chain 'B' and (resseq 139:168)B139 - 168
13X-RAY DIFFRACTION13chain 'B' and (resseq 169:193)B169 - 193
14X-RAY DIFFRACTION14chain 'B' and (resseq 194:221)B194 - 221
15X-RAY DIFFRACTION15chain 'B' and (resseq 222:250)B222 - 250
16X-RAY DIFFRACTION16chain 'B' and (resseq 251:329)B251 - 329
17X-RAY DIFFRACTION17chain 'B' and (resseq 330:368)B330 - 368

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