[English] 日本語
Yorodumi
- PDB-5nx4: Crystal structure of Linalool/Nerolidol synthase from Streptomyce... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5nx4
TitleCrystal structure of Linalool/Nerolidol synthase from Streptomyces clavuligerus
ComponentsPentalenene synthase
KeywordsLIGASE / terpene synthase / linalool / nerolidol / monoterpenoid
Function / homology
Function and homology information


R-linalool synthase / R-linalool synthase activity / geranyl diphosphate metabolic process / farnesyl diphosphate metabolic process / magnesium ion binding
Similarity search - Function
Terpene cyclase-like 2 / Terpene synthase family 2, C-terminal metal binding / Farnesyl Diphosphate Synthase / Farnesyl Diphosphate Synthase / Isoprenoid synthase domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesStreptomyces clavuligerus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.38 Å
AuthorsKaruppiah, V. / Leys, D. / Scrutton, N.S.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research CouncilBB/M000354/1 United Kingdom
CitationJournal: ACS Catal / Year: 2017
Title: Structural Basis of Catalysis in the Bacterial Monoterpene Synthases Linalool Synthase and 1,8-Cineole Synthase.
Authors: Karuppiah, V. / Ranaghan, K.E. / Leferink, N.G.H. / Johannissen, L.O. / Shanmugam, M. / Ni Cheallaigh, A. / Bennett, N.J. / Kearsey, L.J. / Takano, E. / Gardiner, J.M. / van der Kamp, M.W. / ...Authors: Karuppiah, V. / Ranaghan, K.E. / Leferink, N.G.H. / Johannissen, L.O. / Shanmugam, M. / Ni Cheallaigh, A. / Bennett, N.J. / Kearsey, L.J. / Takano, E. / Gardiner, J.M. / van der Kamp, M.W. / Hay, S. / Mulholland, A.J. / Leys, D. / Scrutton, N.S.
History
DepositionMay 9, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 20, 2017Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2017Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.pdbx_database_id_PubMed ..._citation.journal_abbrev / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Jan 17, 2024Group: 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Pentalenene synthase
B: Pentalenene synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,4538
Polymers72,9002
Non-polymers5536
Water4,342241
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4900 Å2
ΔGint-12 kcal/mol
Surface area23300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)140.150, 140.150, 87.180
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number79
Space group name H-MI4

-
Components

#1: Protein Pentalenene synthase / Linalool/Nerolidol synthase


Mass: 36450.055 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces clavuligerus (bacteria) / Gene: SCLAV_p1185 / Production host: Escherichia coli (E. coli) / References: UniProt: D5SL78, pentalenene synthase
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 241 / 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: 2.94 Å3/Da / Density % sol: 58.11 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop / Details: 25% w/v PEG3350

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.92819 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Apr 30, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92819 Å / Relative weight: 1
ReflectionResolution: 2.38→50.9 Å / Num. obs: 33849 / % possible obs: 99.7 % / Redundancy: 4.5 % / CC1/2: 0.998 / Rmerge(I) obs: 0.082 / Rpim(I) all: 0.043 / Net I/σ(I): 14.6
Reflection shellResolution: 2.38→2.42 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.766 / Mean I/σ(I) obs: 1.7 / Num. unique obs: 1697 / CC1/2: 0.576 / Rpim(I) all: 0.44 / % possible all: 99.7

-
Processing

Software
NameVersionClassification
PHENIX(dev_2621: ???)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
PHENIXmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1PS1

1ps1


Resolution: 2.38→50.89 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 22.52
RfactorNum. reflection% reflection
Rfree0.2269 1657 4.9 %
Rwork0.185 --
obs0.187 33844 99.71 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.38→50.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4469 0 36 241 4746
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0024615
X-RAY DIFFRACTIONf_angle_d0.4466264
X-RAY DIFFRACTIONf_dihedral_angle_d9.4132667
X-RAY DIFFRACTIONf_chiral_restr0.032672
X-RAY DIFFRACTIONf_plane_restr0.003811
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3803-2.45030.27311380.25532683X-RAY DIFFRACTION100
2.4503-2.52940.35761330.24742632X-RAY DIFFRACTION99
2.5294-2.61980.27041260.22752679X-RAY DIFFRACTION100
2.6198-2.72470.27841520.22642681X-RAY DIFFRACTION100
2.7247-2.84870.2331270.19542693X-RAY DIFFRACTION100
2.8487-2.99890.27711260.22687X-RAY DIFFRACTION100
2.9989-3.18670.22431400.19292662X-RAY DIFFRACTION100
3.1867-3.43270.21041510.17912656X-RAY DIFFRACTION100
3.4327-3.77810.20641380.15972675X-RAY DIFFRACTION100
3.7781-4.32450.19161180.14882734X-RAY DIFFRACTION100
4.3245-5.44740.1831570.16172678X-RAY DIFFRACTION100
5.4474-50.90180.25421510.20512727X-RAY DIFFRACTION99
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)
11.0475-0.6303-1.12671.07440.90851.283-0.14020.1404-0.4796-0.06150.0081-0.02940.1201-0.2327-00.3439-0.0040.03950.4102-0.04390.412226.7196247.2014-33.7564
21.28131.1758-0.1541.42120.45541.209-0.01010.0172-0.0063-0.08390.00990.05420.0025-0.1835-00.35060.0403-0.00030.39140.03910.351824.3517259.5038-27.3645
30.61260.2190.08750.2662-0.10850.1123-0.0270.06230.0187-0.14870.04860.0350.0803-0.168300.3883-0.00420.01690.33310.01820.393732.0647267.737-23.5253
40.7114-0.16730.38230.63580.35690.53930.032-0.1419-0.00350.0530.0343-0.0969-0.0229-0.044700.34470.0203-0.04690.38490.02030.376336.2095261.0803-17.6126
51.0307-0.33580.07950.2105-0.11230.07750.10810.1323-0.3232-0.09770.0223-0.16610.08690.0162-0.00010.35070.01220.04520.3611-0.0220.46847.4873259.2705-27.0897
60.50460.2129-0.22460.1217-0.27541.1061-0.0219-0.1899-0.36230.0937-0.0441-0.37060.06180.1726-0.00010.38480.0348-0.05520.43580.04410.543143.3536251.153-13.7858
70.95360.18660.471.0762-0.34630.412-0.19310.00090.38160.0502-0.0365-0.3854-0.24290.1019-00.52630.0379-0.10840.531-0.07850.526143.2868296.0735-6.887
81.0889-0.37880.1871.07930.92491.0623-0.2468-0.364-0.03710.19660.1581-0.08360.1327-0.0349-0.00020.41610.0686-0.04370.43070.05470.291334.0104286.6774-5.5138
90.41990.37310.2380.77590.65160.5643-0.0574-0.07580.00030.01960.09840.2213-0.0774-0.204200.38730.0560.00080.35560.01420.305529.4008280.5272-11.2661
100.73810.39350.01670.7508-0.0024-0.0002-0.00180.00860.1242-0.0821-0.0741-0.28210.07370.00310.00010.45580.02080.0130.41870.00580.336340.991278.8985-17.0737
110.50670.6663-0.23951.9524-0.85040.9370.14420.0184-0.11140.1673-0.0673-0.5543-0.12790.39630.00030.39970.0374-0.04850.4271-0.00440.518453.5152276.6393-12.8772
120.2540.2013-0.29210.9503-0.18610.3357-0.1388-0.0390.0755-0.12360.0868-0.3383-0.17210.0896-0.00030.4458-0.01110.03450.42570.0040.521847.9224289.5544-19.7003
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 5 through 47 )
2X-RAY DIFFRACTION2chain 'A' and (resid 48 through 132 )
3X-RAY DIFFRACTION3chain 'A' and (resid 133 through 159 )
4X-RAY DIFFRACTION4chain 'A' and (resid 160 through 200 )
5X-RAY DIFFRACTION5chain 'A' and (resid 201 through 245 )
6X-RAY DIFFRACTION6chain 'A' and (resid 246 through 304 )
7X-RAY DIFFRACTION7chain 'B' and (resid 4 through 31 )
8X-RAY DIFFRACTION8chain 'B' and (resid 32 through 105 )
9X-RAY DIFFRACTION9chain 'B' and (resid 106 through 159 )
10X-RAY DIFFRACTION10chain 'B' and (resid 160 through 200 )
11X-RAY DIFFRACTION11chain 'B' and (resid 201 through 278 )
12X-RAY DIFFRACTION12chain 'B' and (resid 279 through 304 )

+
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