[English] 日本語
Yorodumi
- PDB-5ily: Tobacco 5-epi-aristolochene synthase with BIS-TRIS buffer molecul... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5ily
TitleTobacco 5-epi-aristolochene synthase with BIS-TRIS buffer molecule and diphosphate (PPi)
Components5-epi-aristolochene synthase
KeywordsLYASE / terpene synthase / TEAS / BIS-TRIS / diphosphate
Function / homology
Function and homology information


(+)-2-epi-prezizaene synthase / (-)-alpha-cedrene synthase / 5-epiaristolochene synthase / 5-epi-aristolochene synthase activity / sesquiterpene biosynthetic process / diterpenoid biosynthetic process / terpene synthase activity / magnesium ion binding / cytoplasm
Similarity search - Function
Terpene synthase, N-terminal domain / Terpene synthase, metal-binding domain / Terpene cyclases, class 1, plant / 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 / Farnesyl Diphosphate Synthase ...Terpene synthase, N-terminal domain / Terpene synthase, metal-binding domain / Terpene cyclases, class 1, plant / 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 / Farnesyl Diphosphate Synthase / Farnesyl Diphosphate Synthase / Glycosyltransferase / Alpha/alpha barrel / Isoprenoid synthase domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
DIPHOSPHATE / 5-epi-aristolochene synthase
Similarity search - Component
Biological speciesNicotiana tabacum (common tobacco)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.45 Å
AuthorsKoo, H.J. / Louie, G.V. / Xu, Y. / Bowman, M. / Noel, J.P.
CitationJournal: To Be Published
Title: Small-molecule buffer components can directly affect terpene-synthase activity by interacting with the substrate-binding site of the enzyme
Authors: Koo, H.J. / Louie, G.V. / Xu, Y. / Bowman, M. / Noel, J.P.
History
DepositionMar 5, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 8, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 27, 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_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: 5-epi-aristolochene synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,6586
Polymers63,2021
Non-polymers4565
Water1,15364
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)126.740, 126.740, 124.760
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11A-764-

HOH

-
Components

#1: Protein 5-epi-aristolochene synthase / EAS


Mass: 63201.703 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Nicotiana tabacum (common tobacco) / Gene: EAS3, EAS4 / Plasmid: pH9GW / Details (production host): pET28 derived Gateway vector / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: Q40577, 5-epiaristolochene synthase
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-BTB / 2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / BIS-TRIS BUFFER


Mass: 209.240 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H19NO5 / Comment: pH buffer*YM
#4: Chemical ChemComp-DPO / DIPHOSPHATE


Mass: 173.943 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: O7P2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 64 / 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: 3.97 Å3/Da / Density % sol: 69.04 %
Crystal growTemperature: 278 K / Method: vapor diffusion, hanging drop
Details: Crystallizion reserior:100 mM MOPSO, pH 7, 300 mM Mg Acetate, 13% PEG 8000,Soaked in 50 mM MOPSO (pH 7), 110 mM Mg Acetate, 10% PEG 8000, 10 mM BIS-TRIS (pH 6.5), 1 mM inorganic diphosphate (PPi)

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 19, 2013 / Details: mirrors
RadiationMonochromator: double crystal si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.45→51.2 Å / Num. obs: 35732 / % possible obs: 94.3 % / Redundancy: 9.8 % / CC1/2: 0.997 / Rmerge(I) obs: 0.1459 / Net I/σ(I): 10.36
Reflection shellResolution: 2.45→2.538 Å / Redundancy: 9.8 % / Rmerge(I) obs: 3.322 / Mean I/σ(I) obs: 1.2 / Num. measured obs: 3623 / CC1/2: 0.725 / % possible all: 96.87

-
Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
iMOSFLMdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5IM1

5im1


Resolution: 2.45→51.198 Å / SU ML: 0.32 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 30.54 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2173 1451 4.06 %
Rwork0.1818 --
obs0.1833 35732 94.16 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.45→51.198 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4346 0 26 64 4436
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0094490
X-RAY DIFFRACTIONf_angle_d1.1616077
X-RAY DIFFRACTIONf_dihedral_angle_d17.1281655
X-RAY DIFFRACTIONf_chiral_restr0.044684
X-RAY DIFFRACTIONf_plane_restr0.005768
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.45-2.53760.36581390.33623472X-RAY DIFFRACTION97
2.5376-2.63920.34581370.29563481X-RAY DIFFRACTION97
2.6392-2.75930.36771460.27793451X-RAY DIFFRACTION97
2.7593-2.90470.3161580.25483442X-RAY DIFFRACTION96
2.9047-3.08670.31781400.243446X-RAY DIFFRACTION96
3.0867-3.3250.27811500.22783432X-RAY DIFFRACTION95
3.325-3.65950.23971470.19643424X-RAY DIFFRACTION95
3.6595-4.18880.18431470.15643411X-RAY DIFFRACTION93
4.1888-5.27660.16581420.13673333X-RAY DIFFRACTION90
5.2766-51.20940.15011450.13113389X-RAY DIFFRACTION87
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)
13.7539-1.45870.51554.4366-0.37672.8256-0.0086-0.4698-0.57840.24680.0240.77490.134-0.4082-0.08220.5876-0.07580.05070.3466-0.10470.807329.067155.022221.4937
21.45893.5704-0.01749.3521-2.39999.23530.0779-0.4339-0.36950.95380.0212-0.6580.08081.1337-0.04180.50710.1017-0.1120.4273-0.07680.702550.10459.19726.1201
32.8973-1.6923-0.5992.24032.11287.7276-0.04540.08750.1011-0.07850.2544-0.6736-0.31850.7129-0.15080.4156-0.06890.05520.4418-0.12250.759752.707363.96949.4516
43.5049-0.1697-0.29193.60260.86692.5364-0.0345-0.0149-0.19330.0257-0.17470.9048-0.1382-0.33220.19240.4637-0.04390.08420.3952-0.11890.864423.691863.436818.7957
52.8361-0.6042-0.43972.49540.75811.70270.0199-0.21140.82720.0069-0.08151.224-0.5644-0.50790.01270.75030.09670.07710.5969-0.22591.542617.993887.067223.2468
63.8448-0.4542-1.14847.5822-4.20738.8048-0.04140.23420.7548-0.4219-0.0360.3406-0.4905-0.53320.08090.54960.0271-0.05710.3785-0.16110.952331.665284.047516.0286
72.78330.0302-0.22513.51640.29793.1588-0.09910.22550.2028-0.25270.04880.2321-0.1665-0.03130.05560.42120.0251-0.0040.3582-0.07960.779433.74571.372114.3557
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 13 through 77 )
2X-RAY DIFFRACTION2chain 'A' and (resid 78 through 116 )
3X-RAY DIFFRACTION3chain 'A' and (resid 117 through 195 )
4X-RAY DIFFRACTION4chain 'A' and (resid 196 through 304 )
5X-RAY DIFFRACTION5chain 'A' and (resid 305 through 412 )
6X-RAY DIFFRACTION6chain 'A' and (resid 413 through 472 )
7X-RAY DIFFRACTION7chain 'A' and (resid 473 through 548 )

+
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