[English] 日本語
Yorodumi
- PDB-7kjd: F96M epi-isozizaene synthase: complex with 3 Mg2+ and risedronate -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7kjd
TitleF96M epi-isozizaene synthase: complex with 3 Mg2+ and risedronate
Componentsepi-isozizaene synthase
KeywordsLYASE / terpene cyclase / complex / bisphosphonate inhibitor / risedronate
Function / homology
Function and homology information


epi-isozizaene synthase / epi-isozizaene synthase activity / Lyases; Carbon-oxygen lyases; Acting on phosphates / terpene synthase activity / lyase activity / metal ion binding
Similarity search - Function
: / Terpene cyclase-like 2 / Terpene synthase family 2, C-terminal metal binding / Isoprenoid synthase domain superfamily
Similarity search - Domain/homology
Chem-RIS / Terpene synthase / Epi-isozizaene synthase
Similarity search - Component
Biological speciesStreptomyces coelicolor (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsRonnebaum, T.A. / Gardner, S.M. / Christianson, D.W.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM56838 United States
CitationJournal: Biochemistry / Year: 2020
Title: An Aromatic Cluster in the Active Site of epi -Isozizaene Synthase Is an Electrostatic Toggle for Divergent Terpene Cyclization Pathways.
Authors: Ronnebaum, T.A. / Gardner, S.M. / Christianson, D.W.
History
DepositionOct 26, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 16, 2020Provider: repository / Type: Initial release
Revision 1.1Dec 30, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Oct 18, 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: epi-isozizaene synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,1526
Polymers43,7001
Non-polymers4525
Water4,125229
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1160 Å2
ΔGint-43 kcal/mol
Surface area13360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.820, 47.080, 75.410
Angle α, β, γ (deg.)90.000, 96.310, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

-
Components

#1: Protein epi-isozizaene synthase


Mass: 43700.035 Da / Num. of mol.: 1 / Mutation: F96M
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces coelicolor (bacteria) / Gene: HCU77_26465 / Production host: Escherichia coli (E. coli)
References: UniProt: A0A6M9XZI2, UniProt: Q9K499*PLUS, epi-isozizaene synthase
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-RIS / 1-HYDROXY-2-(3-PYRIDINYL)ETHYLIDENE BIS-PHOSPHONIC ACID / Risedronate


Mass: 283.112 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H11NO7P2 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 229 / 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: 2.13 Å3/Da / Density % sol: 42.32 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop
Details: 0.08 mM Bis-Tris, pH 5.5, 0.02 mM Bis-Tris, pH 7.5, 0.2 M ammonium sulfate, 26% PEG3350, 2% w/v benzamidine HCl

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.978 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jun 26, 2020
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 1.5→52.5 Å / Num. obs: 58620 / % possible obs: 99.1 % / Redundancy: 3.3 % / Biso Wilson estimate: 15.78 Å2 / CC1/2: 0.982 / Net I/σ(I): 6.1
Reflection shellResolution: 1.5→1.53 Å / Num. unique obs: 2892 / CC1/2: 0.694

-
Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
PHENIX1.13_2998refinement
iMOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3KB9

3kb9


Resolution: 1.5→52.5 Å / SU ML: 0.199 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.5284 / Stereochemistry target values: GeoStd + Monomer Library
RfactorNum. reflection% reflection
Rfree0.2458 5853 3.4 %
Rwork0.2152 106288 -
obs0.2163 58547 95.12 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 22.7 Å2
Refinement stepCycle: LAST / Resolution: 1.5→52.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2688 0 25 229 2942
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00552798
X-RAY DIFFRACTIONf_angle_d0.76753829
X-RAY DIFFRACTIONf_chiral_restr0.042406
X-RAY DIFFRACTIONf_plane_restr0.0054493
X-RAY DIFFRACTIONf_dihedral_angle_d5.79722193
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5-1.520.33231450.32344068X-RAY DIFFRACTION97.64
1.52-1.540.32111400.31833945X-RAY DIFFRACTION96.94
1.54-1.560.35111450.2994045X-RAY DIFFRACTION96.66
1.56-1.580.3971410.30763990X-RAY DIFFRACTION96.7
1.58-1.610.30281420.29174040X-RAY DIFFRACTION96.65
1.61-1.630.30871370.27813949X-RAY DIFFRACTION96.62
1.63-1.660.28721410.2863964X-RAY DIFFRACTION96.2
1.66-1.690.35381460.26294060X-RAY DIFFRACTION96.6
1.69-1.720.28651370.26463955X-RAY DIFFRACTION96.42
1.72-1.750.26371390.25643975X-RAY DIFFRACTION95.85
1.75-1.790.26851380.24933876X-RAY DIFFRACTION95.07
1.79-1.820.24841380.24713949X-RAY DIFFRACTION93.72
1.82-1.870.27531350.23743758X-RAY DIFFRACTION91.36
1.87-1.910.27681290.23753600X-RAY DIFFRACTION87.76
1.91-1.970.25581200.22563300X-RAY DIFFRACTION79.09
1.97-2.020.23391310.21833752X-RAY DIFFRACTION89.78
2.02-2.090.26981370.20593973X-RAY DIFFRACTION97.93
2.09-2.160.21641440.20614100X-RAY DIFFRACTION98.35
2.16-2.250.21481430.19974070X-RAY DIFFRACTION98.3
2.25-2.350.2361400.20364100X-RAY DIFFRACTION97.85
2.35-2.480.21161430.20094040X-RAY DIFFRACTION98.28
2.48-2.630.25791400.2054066X-RAY DIFFRACTION97.93
2.63-2.830.21651390.20844016X-RAY DIFFRACTION97.83
2.83-3.120.28521420.20654024X-RAY DIFFRACTION96.59
3.12-3.570.24031340.20073740X-RAY DIFFRACTION90.7
3.57-4.50.22231310.17723868X-RAY DIFFRACTION93.5
4.5-52.50.19561450.19214065X-RAY DIFFRACTION98.25

+
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