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- PDB-7wh9: holo structure of emodin 1-OH O-methyltransferase complex with em... -

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Basic information

Entry
Database: PDB / ID: 7wh9
Titleholo structure of emodin 1-OH O-methyltransferase complex with emodin and S-Adenosyl-L-homocysteine
ComponentsO-methyltransferase gedA
KeywordsTRANSFERASE / O-methyltransferase / emodin
Function / homology
Function and homology information


emodin O-methyltransferase / O-methyltransferase activity / secondary metabolite biosynthetic process / methylation
Similarity search - Function
O-methyltransferase domain / O-methyltransferase domain / SAM-dependent O-methyltransferase class II-type profile. / O-methyltransferase COMT-type / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / S-adenosyl-L-methionine-dependent methyltransferase superfamily
Similarity search - Domain/homology
3-METHYL-1,6,8-TRIHYDROXYANTHRAQUINONE / S-ADENOSYL-L-HOMOCYSTEINE / O-methyltransferase gedA
Similarity search - Component
Biological speciesAspergillus terreus (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.803 Å
AuthorsLiang, Y.J. / Lu, X.F. / Qi, F.F. / Xue, Y.Y.
Funding support China, 2items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31972855 China
Ministry of Science and Technology (MoST, China)2021YFC2102600 China
CitationJournal: J.Agric.Food Chem. / Year: 2022
Title: Characterization and Structural Analysis of Emodin- O -Methyltransferase from Aspergillus terreus.
Authors: Xue, Y. / Liang, Y. / Zhang, W. / Geng, C. / Feng, D. / Huang, X. / Dong, S. / Zhang, Y. / Sun, J. / Qi, F. / Lu, X.
History
DepositionDec 30, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 11, 2023Provider: repository / Type: Initial release
Revision 1.1Jan 18, 2023Group: 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
Revision 1.2May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: O-methyltransferase gedA
B: O-methyltransferase gedA
C: O-methyltransferase gedA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)170,0829
Polymers168,1183
Non-polymers1,9646
Water2,270126
1
A: O-methyltransferase gedA
B: O-methyltransferase gedA
C: O-methyltransferase gedA
hetero molecules

A: O-methyltransferase gedA
B: O-methyltransferase gedA
C: O-methyltransferase gedA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)340,16418
Polymers336,2376
Non-polymers3,92812
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_554x-y,-y,-z-1/31
Buried area45120 Å2
ΔGint-270 kcal/mol
Surface area93780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)162.093, 162.093, 130.219
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resseq 1:36 or (resid 37 and (name...
21(chain B and (resseq 1:39 or resseq 42 or resseq...
31(chain C and (resseq 1:36 or (resid 37 and (name...

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain A and (resseq 1:36 or (resid 37 and (name...A1 - 36
121(chain A and (resseq 1:36 or (resid 37 and (name...A37
131(chain A and (resseq 1:36 or (resid 37 and (name...A1 - 482
141(chain A and (resseq 1:36 or (resid 37 and (name...A1 - 482
151(chain A and (resseq 1:36 or (resid 37 and (name...A1 - 482
161(chain A and (resseq 1:36 or (resid 37 and (name...A1 - 482
211(chain B and (resseq 1:39 or resseq 42 or resseq...B1 - 39
221(chain B and (resseq 1:39 or resseq 42 or resseq...B42
231(chain B and (resseq 1:39 or resseq 42 or resseq...B49 - 112
241(chain B and (resseq 1:39 or resseq 42 or resseq...B1221 - 248
251(chain B and (resseq 1:39 or resseq 42 or resseq...B1 - 482
261(chain B and (resseq 1:39 or resseq 42 or resseq...B1 - 482
271(chain B and (resseq 1:39 or resseq 42 or resseq...B221 - 2480
281(chain B and (resseq 1:39 or resseq 42 or resseq...B1 - 482
291(chain B and (resseq 1:39 or resseq 42 or resseq...B1 - 482
2101(chain B and (resseq 1:39 or resseq 42 or resseq...B1 - 482
2111(chain B and (resseq 1:39 or resseq 42 or resseq...B1 - 482
2121(chain B and (resseq 1:39 or resseq 42 or resseq...B1 - 482
2131(chain B and (resseq 1:39 or resseq 42 or resseq...B1 - 482
311(chain C and (resseq 1:36 or (resid 37 and (name...C1 - 36
321(chain C and (resseq 1:36 or (resid 37 and (name...C37
331(chain C and (resseq 1:36 or (resid 37 and (name...C1 - 482
341(chain C and (resseq 1:36 or (resid 37 and (name...C1 - 482

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Components

#1: Protein O-methyltransferase gedA / Geodin synthesis protein A


Mass: 56039.434 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aspergillus terreus (mold) / Strain: NIH 2624 / FGSC A1156 / Gene: gedA, ATEG_08449 / Production host: Escherichia coli (E. coli) / References: UniProt: Q0CCY5, emodin O-methyltransferase
#2: Chemical ChemComp-EMO / 3-METHYL-1,6,8-TRIHYDROXYANTHRAQUINONE / EMODIN


Mass: 270.237 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C15H10O5 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE


Type: L-peptide linking / Mass: 384.411 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C14H20N6O5S / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 126 / 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: 2

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Sample preparation

Crystal
IDDensity Matthews (Å3/Da)Density % sol (%)
12.8858.13
22.1743.4
Crystal grow
Temperature (K)Crystal-IDMethodpHDetails
289.151vapor diffusion, hanging drop71.8M triamine citrate
289.152vapor diffusion, sitting drop61.8M triamine citrate

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Data collection

Diffraction
IDMean temperature (K)Crystal-IDSerial crystal experiment
11001N
21001N
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONSSRF BL19U110.979
SYNCHROTRONSSRF BL17U120.979
Detector
TypeIDDetectorDate
DECTRIS PILATUS 6M1PIXELApr 18, 2019
DECTRIS EIGER X 16M2PIXELJun 26, 2019
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2SINGLE WAVELENGTHMx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
10.9791
21
ReflectionResolution: 2.8→30 Å / Num. obs: 48697 / % possible obs: 99.9 % / Redundancy: 10.3 % / CC1/2: 0.997 / Rmerge(I) obs: 0.109 / Rpim(I) all: 0.035 / Rrim(I) all: 0.115 / Net I/σ(I): 24.5
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 10.7 % / Rmerge(I) obs: 0.501 / Mean I/σ(I) obs: 4.5 / Num. unique obs: 4803 / CC1/2: 0.94 / Rpim(I) all: 0.161 / Rrim(I) all: 0.526 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
HKL-3000data scaling
xia2data scaling
PDB_EXTRACT3.27data extraction
HKL-3000data reduction
xia2data reduction
PHASERphasing
AutoSolphasing
RefinementMethod to determine structure: SAD / Resolution: 2.803→27.2917 Å / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 21.62 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2172 1994 4.11 %
Rwork0.1748 46509 -
obs0.1766 48503 99.57 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 165.9 Å2 / Biso mean: 61.6619 Å2 / Biso min: 14.95 Å2
Refinement stepCycle: final / Resolution: 2.803→27.2917 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10992 0 138 126 11256
Biso mean--54.1 38.15 -
Num. residues----1423
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01111474
X-RAY DIFFRACTIONf_angle_d1.32715610
X-RAY DIFFRACTIONf_chiral_restr0.0831749
X-RAY DIFFRACTIONf_plane_restr0.0112015
X-RAY DIFFRACTIONf_dihedral_angle_d18.4516858
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A6486X-RAY DIFFRACTION10.614TORSIONAL
12B6486X-RAY DIFFRACTION10.614TORSIONAL
13C6486X-RAY DIFFRACTION10.614TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.8031-2.87310.27861390.231432913430100
2.8731-2.95070.26611420.224733073449100
2.9507-3.03740.28491430.221632943437100
3.0374-3.13530.25481420.224832993441100
3.1353-3.24720.30781400.212133143454100
3.2472-3.3770.25781420.200133063448100
3.377-3.53040.22751450.19073264340999
3.5304-3.71610.20181410.171333223463100
3.7161-3.94820.21881440.166633223466100
3.9482-4.2520.17881420.155333273469100
4.252-4.6780.20151380.137133303468100
4.678-5.35050.18881450.153933563501100
5.3505-6.72430.19921430.17853383352699
6.7243-27.29170.18471480.1533394354297
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)
11.9633-0.2016-0.73671.8240.46113.0747-0.1587-0.01020.2396-0.10940.2106-0.0252-0.38860.3488-0.04040.12410.013-0.02940.270.10490.329646.87243.0254-23.7222
23.57150.2337-0.25482.6065-0.9390.9769-0.1794-0.07020.4829-0.09790.2742-0.0215-0.34020.3651-0.14530.1704-0.0093-0.05110.3250.08250.289641.859811.3456-20.5315
31.3643-0.7459-1.43641.86121.42632.05360.0377-0.20560.08730.13990.1303-0.2119-0.0820.1773-0.10470.17970.0104-0.06220.20320.03520.18424.9910.0269-11.1688
40.8048-0.1419-0.01640.60960.21370.8096-0.0697-0.11470.05710.07170.02030.0068-0.0409-0.05410.0370.17890.01120.0020.17970.04050.181714.57527.7021-13.9185
53.233-0.2612-0.06711.2161-0.31131.4407-0.1182-0.17040.32850.11670.1089-0.2284-0.45470.2561-0.03010.3466-0.0664-0.03820.22820.01460.351927.425333.3448-17.9808
66.08481.30391.38886.374-0.65936.52920.1621-0.29350.41041.0795-0.3347-0.1614-0.78170.05540.15940.39120.05540.00750.27620.00190.344516.679333.1819-9.5132
71.36430.0806-0.32091.47990.35351.0899-0.03040.18350.2785-0.21920.105-0.127-0.27480.066-0.07120.2756-0.0412-0.00410.25190.07730.262725.635524.3427-31.9265
83.90860.5962-1.13192.8181-0.5951.9925-0.0773-0.2232-0.64030.34680.02220.1674-0.0209-0.0385-0.06820.28340.0277-0.08340.61250.03580.310768.9192.1377-4.307
93.2030.1830.3761.7371-0.46441.5675-0.023-1.3659-0.03340.56330.12530.0877-0.0018-0.3832-0.06170.43170.0722-0.04691.17790.0580.407974.37086.067521.4923
102.84260.2960.93682.52110.02490.7565-0.15480.60210.2949-0.3620.0556-0.2983-0.18280.16560.13790.3205-0.0096-0.05960.57410.09440.309673.635311.9587-12.5073
116.5558-0.00490.43062.20340.01052.2530.0364-0.1901-0.18860.03170.03-0.55910.09220.2421-0.06480.25620.0132-0.04950.5029-0.00880.375291.77745.7536.347
123.96810.75370.70550.94910.00511.4006-0.1174-0.6530.66040.21830.0233-0.2716-0.2866-0.10630.06120.36310.0731-0.13350.5869-0.11360.558292.739219.218510.3823
133.14260.27050.86771.33410.16980.9688-0.45730.50341.3676-0.17750.1308-0.0769-0.47740.0060.33850.4496-0.1527-0.14330.66020.16280.9987100.029128.7425-6.1869
143.0921-0.2096-1.16343.5278-0.07923.8175-0.37810.81881.2507-0.7292-0.1035-0.8937-0.48030.86660.32120.526-0.1475-0.09780.97280.22821.3706108.624631.6344-8.8158
151.3932-0.2975-0.3252.00820.31041.3827-0.43830.30811.6191-0.16770.1521-0.0571-0.7809-0.00250.24510.6507-0.0262-0.3190.6420.14491.362883.72336.8992-5.9121
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 41 )A1 - 41
2X-RAY DIFFRACTION2chain 'A' and (resid 42 through 79 )A42 - 79
3X-RAY DIFFRACTION3chain 'A' and (resid 80 through 119 )A80 - 119
4X-RAY DIFFRACTION4chain 'A' and (resid 120 through 276 )A120 - 276
5X-RAY DIFFRACTION5chain 'A' and (resid 277 through 322 )A277 - 322
6X-RAY DIFFRACTION6chain 'A' and (resid 323 through 351 )A323 - 351
7X-RAY DIFFRACTION7chain 'A' and (resid 352 through 482 )A352 - 482
8X-RAY DIFFRACTION8chain 'B' and (resid 1 through 79 )B1 - 79
9X-RAY DIFFRACTION9chain 'B' and (resid 80 through 482 )B80 - 482
10X-RAY DIFFRACTION10chain 'C' and (resid 1 through 79 )C1 - 79
11X-RAY DIFFRACTION11chain 'C' and (resid 80 through 130 )C80 - 130
12X-RAY DIFFRACTION12chain 'C' and (resid 131 through 241 )C131 - 241
13X-RAY DIFFRACTION13chain 'C' and (resid 242 through 322 )C242 - 322
14X-RAY DIFFRACTION14chain 'C' and (resid 323 through 351 )C323 - 351
15X-RAY DIFFRACTION15chain 'C' and (resid 352 through 482 )C352 - 482

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