[English] 日本語
Yorodumi
- PDB-7wh9: holo structure of emodin 1-OH O-methyltransferase complex with em... -

+
Open data


ID or keywords:

Loading...

-
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 COMT-type / O-methyltransferase domain / SAM-dependent O-methyltransferase class II-type profile. / 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

-
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

-
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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

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

Read more