[English] 日本語
Yorodumi
- PDB-7cjy: Drimenol synthase from Persicaria hydropiper -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7cjy
TitleDrimenol synthase from Persicaria hydropiper
Components(-)-drimenol synthase
KeywordsBIOSYNTHETIC PROTEIN / terpene synthase / sesquiterpene synthase / drimane / terpene / sesquiterpene
Function / homology
Function and homology information


(-)-drimenol synthase / terpene synthase activity / terpenoid biosynthetic process / magnesium ion binding
Similarity search - Function
Terpene cyclase-like 1, C-terminal domain / Terpene synthase, metal-binding domain / Terpene synthase family, metal binding domain / Terpene synthase, N-terminal domain / Terpene synthase, N-terminal domain superfamily / Terpene synthase, N-terminal domain / Terpenoid cyclases/protein prenyltransferase alpha-alpha toroid / Isoprenoid synthase domain superfamily
Similarity search - Domain/homology
(-)-drimenol synthase
Similarity search - Component
Biological speciesPersicaria hydropiper (water-pepper)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsXiao, W. / Zhou, H. / Zhou, M.T. / Liu, L. / Xiang, Z.
CitationJournal: To Be Published
Title: Structural and Biochemical Studies of Drimenol Synthase from Persicaria hydropiper
Authors: Xiao, W. / Zhou, H. / Zhou, M.T. / Liu, L. / Xiang, Z.
History
DepositionJul 14, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 14, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: (-)-drimenol synthase
B: (-)-drimenol synthase


Theoretical massNumber of molelcules
Total (without water)125,9942
Polymers125,9942
Non-polymers00
Water1,02757
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4820 Å2
ΔGint-28 kcal/mol
Surface area44760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)232.530, 60.090, 106.220
Angle α, β, γ (deg.)90.000, 111.875, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLYGLYASPASP(chain 'A' and (resid 18 through 174 or resid 176...AA18 - 1741 - 157
12ALAALASERSER(chain 'A' and (resid 18 through 174 or resid 176...AA176 - 257159 - 240
13TRPTRPPHEPHE(chain 'A' and (resid 18 through 174 or resid 176...AA259 - 282242 - 265
14THRTHRARGARG(chain 'A' and (resid 18 through 174 or resid 176...AA284 - 376267 - 359
15GLUGLUILEILE(chain 'A' and (resid 18 through 174 or resid 176...AA378 - 380361 - 363
16METMETGLUGLU(chain 'A' and (resid 18 through 174 or resid 176...AA382 - 535365 - 518
17TYRTYRILEILE(chain 'A' and (resid 18 through 174 or resid 176...AA538 - 559521 - 542
21GLYGLYASPASP(chain 'B' and (resid 18 through 174 or resid 176...BB18 - 1741 - 157
22ALAALASERSER(chain 'B' and (resid 18 through 174 or resid 176...BB176 - 257159 - 240
23TRPTRPPHEPHE(chain 'B' and (resid 18 through 174 or resid 176...BB259 - 282242 - 265
24THRTHRARGARG(chain 'B' and (resid 18 through 174 or resid 176...BB284 - 376267 - 359
25GLUGLUILEILE(chain 'B' and (resid 18 through 174 or resid 176...BB378 - 380361 - 363
26METMETGLUGLU(chain 'B' and (resid 18 through 174 or resid 176...BB382 - 535365 - 518
27TYRTYRILEILE(chain 'B' and (resid 18 through 174 or resid 176...BB538 - 559521 - 542

-
Components

#1: Protein (-)-drimenol synthase / PhDS / Drimenol cyclase / Sesquiterpene synthase


Mass: 62996.918 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Persicaria hydropiper (water-pepper) / Production host: Escherichia coli (E. coli) / References: UniProt: W0FFD7, (-)-drimenol synthase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 57 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.66 Å3/Da / Density % sol: 53.69 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 22.5% w/v PEG 3000, 0.1 M citrate, pH 5.5, 0.2 M ammonium acetate, 10% v/v glycerol

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.979 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 17, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.2→28.74 Å / Num. obs: 69159 / % possible obs: 98.97 % / Redundancy: 6.6 % / Biso Wilson estimate: 51.84 Å2 / CC1/2: 0.995 / CC star: 0.999 / Rmerge(I) obs: 0.08643 / Rpim(I) all: 0.03731 / Rrim(I) all: 0.0944 / Net I/σ(I): 12.09
Reflection shellResolution: 2.2→2.279 Å / Redundancy: 6.8 % / Rmerge(I) obs: 0.5677 / Mean I/σ(I) obs: 2.72 / Num. unique obs: 6797 / CC1/2: 0.961 / CC star: 0.99 / Rpim(I) all: 0.237 / Rrim(I) all: 0.6161 / % possible all: 98.56

-
Processing

Software
NameVersionClassification
Blu-Icedata collection
XDSdata processing
PHASERphasing
PHENIX1.17.1refinement
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5EAU

5eau


Resolution: 2.2→28.74 Å / SU ML: 0.2793 / Cross valid method: FREE R-VALUE / σ(F): 0.01 / Phase error: 32.339
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2338 3435 4.98 %
Rwork0.1947 126494 -
obs0.1966 68963 98.31 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 71.23 Å2
Refinement stepCycle: LAST / Resolution: 2.2→28.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8803 0 0 57 8860
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00779094
X-RAY DIFFRACTIONf_angle_d0.953312306
X-RAY DIFFRACTIONf_chiral_restr0.05451298
X-RAY DIFFRACTIONf_plane_restr0.00711582
X-RAY DIFFRACTIONf_dihedral_angle_d24.52943384
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.220.3652430.29394289X-RAY DIFFRACTION98.12
2.23-2.250.34792270.28194118X-RAY DIFFRACTION98.13
2.25-2.280.37172190.30194128X-RAY DIFFRACTION98.08
2.28-2.310.34822400.29094333X-RAY DIFFRACTION97.92
2.31-2.340.332590.28684092X-RAY DIFFRACTION98.15
2.34-2.370.35331980.28734200X-RAY DIFFRACTION98.39
2.37-2.40.32642450.27774304X-RAY DIFFRACTION98.78
2.4-2.440.29322070.28224180X-RAY DIFFRACTION98.28
2.44-2.480.33722240.26974199X-RAY DIFFRACTION98.97
2.48-2.520.30511990.27864268X-RAY DIFFRACTION98.52
2.52-2.560.37482350.27964206X-RAY DIFFRACTION98.54
2.56-2.610.31552460.27944306X-RAY DIFFRACTION99.02
2.61-2.660.32992180.25714163X-RAY DIFFRACTION98.74
2.66-2.710.271950.24614302X-RAY DIFFRACTION98.6
2.71-2.770.30242180.25524207X-RAY DIFFRACTION99.37
2.77-2.840.26012350.22894278X-RAY DIFFRACTION99.38
2.84-2.910.27632360.23254264X-RAY DIFFRACTION99.38
2.91-2.990.26592100.22864266X-RAY DIFFRACTION99.11
2.99-3.070.31172360.23354200X-RAY DIFFRACTION99.24
3.07-3.170.26852280.23794230X-RAY DIFFRACTION98.32
3.17-3.290.28352330.2444174X-RAY DIFFRACTION97.54
3.29-3.420.28062430.23464196X-RAY DIFFRACTION98.64
3.42-3.570.24941900.20624273X-RAY DIFFRACTION98.61
3.57-3.760.23022070.18924271X-RAY DIFFRACTION98.2
3.76-3.990.21632170.17034180X-RAY DIFFRACTION97.97
3.99-4.30.17641970.15954179X-RAY DIFFRACTION97.07
4.3-4.730.18982120.1474211X-RAY DIFFRACTION98.6
4.73-5.410.16052150.15354229X-RAY DIFFRACTION98.36
5.41-6.810.2052010.17124223X-RAY DIFFRACTION97.77
6.81-28.940.15662110.13214025X-RAY DIFFRACTION93.76
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)
11.674291241870.2962850152590.1134768192691.635664213060.6220059874692.48081218775-0.0135331812116-0.679627507558-0.08702540324610.191138103246-0.08121130738470.161598713541-0.132760990849-0.2372550021540.1087223739080.3758792153820.0785470004059-0.003889327235380.6045404014320.1026955064840.478862829018-49.6073589417-16.478405917660.7141260018
21.644201267540.05964965949930.5150564424370.742315962723-0.2721626269031.45404589837-0.0605413122107-0.1718586096190.0786399403291-0.1163540370880.1051490422250.259955905003-0.212769515963-0.490954537535-0.04679583885180.4806151745780.080076796702-0.004428304228460.5275933575620.07848894047150.643996455624-62.4724575305-12.064157460338.9651533451
33.932541047695.13809630126-1.044470959677.615889888410.586080938255.01391367111-0.3348454138830.1337440825650.223846723856-1.184181546450.4197579338120.595127625349-0.01783836460850.285972514601-0.07512412946970.395536646070.02026526579440.02052175240840.5039920665070.09214181059950.615109223523-48.6752713322-23.962777277440.5617356706
42.90369383037-0.4005697872830.2868545681131.71715409288-0.3678857693811.757528984940.02176897856360.3640555797880.0377550442188-0.208244171164-0.0552548281591-0.186492903999-0.09006830686380.5360744124810.05406189890450.456686026163-0.06008062769490.004054060532270.550612253863-0.03750918938420.399754183748-20.0464240763-16.70055394717.4194550545
51.397743821230.3057219675170.5838916080531.59515693904-0.6192982688932.139329383410.03792928783420.243717306575-0.153522482031-0.3452351172960.1091379973830.2860455074780.25629873037-0.106516168424-0.149739504030.665875085991-0.0192096946718-0.137074408770.467407906115-0.06942052250320.553899514162-44.2059277274-27.99310408058.40088333994
65.58487507626-1.68633939923-0.0449153663095.03332745498-4.076556160653.69484050156-0.0875363095726-0.2474434152140.253779637756-0.1734655351610.4772340203480.9819086012340.1460086582330.0705234325356-0.4858287446330.55173706954-0.0335207830062-0.07621279412190.459532706611-0.03013452928780.469873482393-35.6458249599-12.209026534723.4172887214
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 18:194)
2X-RAY DIFFRACTION2(chain A and resid 195:532)
3X-RAY DIFFRACTION3(chain A and resid 533:559)
4X-RAY DIFFRACTION4(chain B and resid 18:265)
5X-RAY DIFFRACTION5(chain B and resid 266:532)
6X-RAY DIFFRACTION6(chain B and resid 533:559)

+
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://pdbjlvh1.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