[English] 日本語
Yorodumi
- PDB-6thm: Linalool Dehydratase Isomerase M125A mutant -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6thm
TitleLinalool Dehydratase Isomerase M125A mutant
ComponentsLinalool dehydratase-isomerase protein LDI
KeywordsLYASE / Alkene / Alkenol / Hydratase
Function / homology
Function and homology information


linalool dehydratase / geraniol isomerase / monoterpene catabolic process / intramolecular hydroxytransferase activity / monoterpenoid metabolic process / hydro-lyase activity / cellular response to organic substance / protein tetramerization / periplasmic space
Similarity search - Function
Linalool dehydratase/isomerase / Linalool dehydratase/isomerase
Similarity search - Domain/homology
MALONATE ION / Linalool dehydratase/isomerase
Similarity search - Component
Biological speciesCastellaniella defragrans 65Phen (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.99 Å
AuthorsCuetos, A. / Zukic, E. / Danesh-Azari, H.R. / Grogan, G.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research CouncilBB/P005578/1 United Kingdom
CitationJournal: Acs Catalysis / Year: 2020
Title: Mutational Analysis of Linalool Dehydratase Isomerase Suggests That Alcohol and Alkene Transformations Are Catalyzed Using Noncovalent Mechanisms
Authors: Cuetos, A. / Iglesias-Fernandez, J. / Danesh-Azari, H.R. / Zukic, E. / Dowle, A. / Osuna, S. / Grogan, G.
History
DepositionNov 20, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 7, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 24, 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: Linalool dehydratase-isomerase protein LDI
B: Linalool dehydratase-isomerase protein LDI
C: Linalool dehydratase-isomerase protein LDI
D: Linalool dehydratase-isomerase protein LDI
E: Linalool dehydratase-isomerase protein LDI
hetero molecules


Theoretical massNumber of molelcules
Total (without water)210,80322
Polymers209,6685
Non-polymers1,13517
Water14,844824
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14210 Å2
ΔGint-23 kcal/mol
Surface area61360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)108.670, 110.689, 196.715
Angle α, β, γ (deg.)90.000, 91.260, 90.000
Int Tables number5
Space group name H-MI121
Components on special symmetry positions
IDModelComponents
11A-638-

HOH

21A-644-

HOH

-
Components

#1: Protein
Linalool dehydratase-isomerase protein LDI


Mass: 41933.598 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Details: M125A mutant
Source: (gene. exp.) Castellaniella defragrans 65Phen (bacteria)
Gene: BN940_14136 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: W8X534
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-MLI / MALONATE ION / Malonic acid


Mass: 102.046 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H2O4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 824 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.82 Å3/Da / Density % sol: 56.39 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.2 M sodium malonate; 0.1 M bis-tris propane pH 7.5; 20% (w/w) PEG3350; 5% (v/v) methylpentanediol

-
Data collection

DiffractionMean temperature: 120 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97625 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: May 20, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 1.99→98.33 Å / Num. obs: 156439 / % possible obs: 98.4 % / Redundancy: 4.2 % / CC1/2: 1 / Rmerge(I) obs: 0.08 / Rpim(I) all: 0.07 / Net I/σ(I): 9.1
Reflection shellResolution: 1.99→2.02 Å / Rmerge(I) obs: 0.91 / Mean I/σ(I) obs: 1.6 / Num. unique obs: 7677 / CC1/2: 0.68 / Rpim(I) all: 0.77

-
Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5G1U

5g1u


Resolution: 1.99→96.18 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.947 / SU B: 4.662 / SU ML: 0.122 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.152 / ESU R Free: 0.141
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.215 7886 5 %RANDOM
Rwork0.178 ---
obs0.1799 148547 98.15 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 95.42 Å2 / Biso mean: 33.191 Å2 / Biso min: 21.02 Å2
Baniso -1Baniso -2Baniso -3
1--3.1 Å20 Å20.13 Å2
2--2.37 Å20 Å2
3---0.72 Å2
Refinement stepCycle: final / Resolution: 1.99→96.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14416 0 74 824 15314
Biso mean--56.99 39.26 -
Num. residues----1825
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.01314932
X-RAY DIFFRACTIONr_bond_other_d0.0010.01713437
X-RAY DIFFRACTIONr_angle_refined_deg1.5421.64420296
X-RAY DIFFRACTIONr_angle_other_deg1.3921.56731023
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.73551824
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.28421.536781
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.988152248
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.3151594
X-RAY DIFFRACTIONr_chiral_restr0.0830.21865
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0216869
X-RAY DIFFRACTIONr_gen_planes_other0.0010.023397
LS refinement shellResolution: 1.99→2.042 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.325 543 -
Rwork0.302 10930 -
all-11473 -
obs--97.37 %

+
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