[English] 日本語
Yorodumi
- PDB-6loo: Crystal Structure of Class IB terpene synthase bound with geranyl... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6loo
TitleCrystal Structure of Class IB terpene synthase bound with geranylcitronellyl diphosphate
ComponentsTetraprenyl-beta-curcumene synthase
KeywordsLYASE / TERPENE SYNTHASE
Function / homologyTetraprenyl-beta-curcumene synthase YtpB-like / Protein of unknown function (DUF2600) / Chem-ELR / Chem-ELU / Tetraprenyl-beta-curcumene synthase
Function and homology information
Biological speciesBacillus alcalophilus ATCC 27647 = CGMCC 1.3604 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.99 Å
AuthorsFujihashi, M. / Inagi, H. / Miki, K.
Funding support Japan, 2items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)17H05439 Japan
Japan Society for the Promotion of Science (JSPS)19H04652 Japan
CitationJournal: Acs Chem.Biol. / Year: 2020
Title: Characterization of Class IB Terpene Synthase: The First Crystal Structure Bound with a Substrate Surrogate.
Authors: Stepanova, R. / Inagi, H. / Sugawara, K. / Asada, K. / Nishi, T. / Ueda, D. / Yasuno, Y. / Shinada, T. / Miki, K. / Fujihashi, M. / Sato, T.
History
DepositionJan 7, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 18, 2020Provider: 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Tetraprenyl-beta-curcumene synthase
B: Tetraprenyl-beta-curcumene synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,1175
Polymers83,7592
Non-polymers1,3573
Water6,539363
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, Gel-filtration chart can be seen on Fig. S3 on Fujihashi, M. et al (2018), 9, 3754-8, doi: 10.1039/C8SC00289D
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1740 Å2
ΔGint-22 kcal/mol
Surface area29300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.870, 53.480, 76.540
Angle α, β, γ (deg.)94.630, 104.720, 113.330
Int Tables number1
Space group name H-MP1

-
Components

#1: Protein Tetraprenyl-beta-curcumene synthase / beta-C25/C30/C35-prene synthase


Mass: 41879.664 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus alcalophilus ATCC 27647 = CGMCC 1.3604 (bacteria)
Gene: BALCAV_0202405 / Plasmid: pColdII / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): pLysS / References: UniProt: A0A094YZ24
#2: Chemical ChemComp-ELR / phosphono [(3~{S},6~{E},10~{E})-3,7,11,15-tetramethylhexadeca-6,10,14-trienyl] hydrogen phosphate


Mass: 452.459 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C20H38O7P2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-ELU / phosphono [(3~{R},6~{E},10~{E})-3,7,11,15-tetramethylhexadeca-6,10,14-trienyl] hydrogen phosphate


Mass: 452.459 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H38O7P2 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 363 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.16 Å3/Da / Density % sol: 43.09 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 8.3
Details: PEG3350, Ammonium Acetate, Magnesium Chloride, Methanol

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B1 / Wavelength: 1 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Oct 31, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.99→48.12 Å / Num. obs: 47141 / % possible obs: 97.8 % / Redundancy: 3.905 % / Biso Wilson estimate: 34.108 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.095 / Rrim(I) all: 0.11 / Χ2: 0.983 / Net I/σ(I): 13.65 / Num. measured all: 184069 / Scaling rejects: 73
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
1.99-2.043.930.842213682360434810.5320.97896.6
2.04-2.13.9230.6312.7513115346333430.6950.73296.5
2.1-2.163.9410.5643.1812734333532310.7660.65396.9
2.16-2.223.9410.4524.0512746332232340.8580.52397.4
2.22-2.33.9230.4174.6412247321331220.8860.48397.2
2.3-2.383.9360.3515.4711626303629540.9350.40697.3
2.38-2.473.9360.2856.511394296028950.9480.3397.8
2.47-2.573.9340.2447.6310972285727890.9670.28397.6
2.57-2.683.9290.1810.0610643276727090.9810.20997.9
2.68-2.813.9290.14611.8610077261225650.9860.1798.2
2.81-2.973.920.12513.599585248524450.990.14498.4
2.97-3.153.9150.09616.399098237023240.9930.11198.1
3.15-3.363.9150.06722.018574222021900.9950.07898.6
3.36-3.633.8830.04827.537852205220220.9980.05598.5
3.63-3.983.8580.03833.787125186418470.9980.04499.1
3.98-4.453.8410.03237.136615173217220.9990.03799.4
4.45-5.143.8170.02740.425649149614800.9990.03298.9
5.14-6.293.7990.02937.24870128912820.9990.03499.5
6.29-8.93.6940.02642.1236099819770.9990.0399.6
8.9-48.123.5090.02448.1218565395290.9980.02898.1

-
Processing

Software
NameVersionClassification
XSCALEdata scaling
REFMAC5.8.0238refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5yo8

5yo8


Resolution: 1.99→48.12 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.941 / SU B: 5.473 / SU ML: 0.146 / SU R Cruickshank DPI: 0.2116 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.212 / ESU R Free: 0.173
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2246 2339 5 %RANDOM
Rwork0.179 ---
obs0.1813 44802 97.88 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 112.86 Å2 / Biso mean: 32.585 Å2 / Biso min: 17.24 Å2
Baniso -1Baniso -2Baniso -3
1-1.49 Å20.76 Å2-0.11 Å2
2---0.93 Å20.28 Å2
3----0.78 Å2
Refinement stepCycle: final / Resolution: 1.99→48.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5767 0 116 363 6246
Biso mean--74.64 38.72 -
Num. residues----694
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0136230
X-RAY DIFFRACTIONr_bond_other_d0.0010.0175644
X-RAY DIFFRACTIONr_angle_refined_deg1.321.6688457
X-RAY DIFFRACTIONr_angle_other_deg1.2811.60713140
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6635730
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.35523.175359
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.514151082
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.0321533
X-RAY DIFFRACTIONr_chiral_restr0.0720.2757
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.026966
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021341
LS refinement shellResolution: 1.99→2.042 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.326 193 -
Rwork0.283 3279 -
all-3472 -
obs--96.39 %

+
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