[English] 日本語
Yorodumi
- PDB-9hqd: T-Muurolol Synthase from Roseiflexus castenholzii (TmS) in comple... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9hqd
TitleT-Muurolol Synthase from Roseiflexus castenholzii (TmS) in complex with 2,3-DHFPP [P2(1)2(1)2(1)]
Components(+)-T-muurolol synthase ((2E,6E)-farnesyl diphosphate cyclizing)
KeywordsLYASE / Biosynthesis / Terpenes / Type I Cyclase / Isomerization / Carbocation Chemistry / Catalysis
Function / homology(+)-T-muurolol synthase / Terpene cyclase-like 2 / terpene synthase activity / Terpene synthase family 2, C-terminal metal binding / terpenoid biosynthetic process / Isoprenoid synthase domain superfamily / metal ion binding / Chem-3E9 / (+)-T-muurolol synthase ((2E,6E)-farnesyl diphosphate cyclizing)
Function and homology information
Biological speciesRoseiflexus castenholzii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsGroll, M. / Li, H. / Troycke, P. / Dickschat, J.S.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG)GR 1861/13-1 Germany
CitationJournal: J.Am.Chem.Soc. / Year: 2025
Title: Structural Mimics of Hydrocarbon Intermediates Reveal Counterclockwise Cyclization Pathways in the Sesquiterpene Synthases TmS and NcECS.
Authors: Groll, M. / Li, H. / Troycke, P. / Kaila, V.R.I. / Dickschat, J.S.
History
DepositionDec 16, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 24, 2025Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: (+)-T-muurolol synthase ((2E,6E)-farnesyl diphosphate cyclizing)
B: (+)-T-muurolol synthase ((2E,6E)-farnesyl diphosphate cyclizing)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,44216
Polymers77,0802
Non-polymers1,36214
Water3,117173
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3600 Å2
ΔGint-9 kcal/mol
Surface area25430 Å2
Unit cell
Length a, b, c (Å)60.430, 75.130, 134.180
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein (+)-T-muurolol synthase ((2E,6E)-farnesyl diphosphate cyclizing) / Terpene cyclase / Type I terpene cyclase


Mass: 38539.812 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Roseiflexus castenholzii (bacteria) / Gene: Rcas_0622 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A7NH01, (+)-T-muurolol synthase
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-3E9 / (3S,6E)-3,7,11-trimethyldodeca-6,10-dien-1-yl trihydrogen diphosphate


Mass: 384.342 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H30O7P2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 173 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 1.98 Å3/Da / Density % sol: 37.75 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: 0.1 M Tris; 0.05 M MgCl2; 25% PEG 1000

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Sep 10, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.8→30 Å / Num. obs: 56395 / % possible obs: 98.1 % / Redundancy: 4.1 % / Rmerge(I) obs: 0.059 / Net I/σ(I): 12.4
Reflection shellResolution: 1.8→1.9 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.679 / Num. unique obs: 8473 / % possible all: 99.8

-
Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→30 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.952 / SU B: 7.577 / SU ML: 0.102 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.273 / ESU R Free: 0.126 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2193 2816 5 %RANDOM
Rwork0.1826 ---
obs0.1846 53506 98.08 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 107.93 Å2 / Biso mean: 39.232 Å2 / Biso min: 19.3 Å2
Baniso -1Baniso -2Baniso -3
1-2.02 Å20 Å20 Å2
2--0.7 Å2-0 Å2
3----2.72 Å2
Refinement stepCycle: final / Resolution: 1.8→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4827 0 84 173 5084
Biso mean--47.78 40.42 -
Num. residues----597
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0020.0135016
X-RAY DIFFRACTIONr_bond_other_d0.0010.0154699
X-RAY DIFFRACTIONr_angle_refined_deg1.1591.6436805
X-RAY DIFFRACTIONr_angle_other_deg1.1571.57410683
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.8135592
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.14520.062321
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.31415774
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.681556
X-RAY DIFFRACTIONr_chiral_restr0.0490.2638
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.025705
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021319
X-RAY DIFFRACTIONr_rigid_bond_restr0.57839715
LS refinement shellResolution: 1.8→1.847 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.344 209 -
Rwork0.275 3967 -
all-4176 -
obs--99.9 %
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)
10.378-0.07680.01790.3635-0.04640.3994-0.02640.04980.01570.00020.02070.06270.04910.03320.00580.01310.00040.00040.01250.01240.07026.70272.12650.2472
20.199-0.1027-0.01180.09280.19631.3030.001-0.0114-0.03370.00880.00770.0131-0.2164-0.0407-0.00870.15970.00760.00430.0057-0.00290.013811.48847.391-36.9616
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 993
2X-RAY DIFFRACTION2B5 - 993

+
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