[English] 日本語
Yorodumi
- PDB-8su0: Unliganded F96H epi-Isozizaene Synthase -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8su0
TitleUnliganded F96H epi-Isozizaene Synthase
ComponentsEpi-isozizaene synthase
KeywordsLYASE / Terpene / Terpenoid / Isoprenoid / Terpene cyclase / Terpene synthase
Function / homologyepi-isozizaene synthase / epi-isozizaene synthase activity / Terpene cyclase-like 2 / terpene synthase activity / Terpene synthase family 2, C-terminal metal binding / Isoprenoid synthase domain superfamily / metal ion binding / Epi-isozizaene synthase
Function and homology information
Biological speciesStreptomyces coelicolor A3
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.99 Å
AuthorsEaton, S.A. / 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: 2023
Title: Reprogramming the Cyclization Cascade of epi -Isozizaene Synthase to Generate Alternative Terpene Products.
Authors: Eaton, S.A. / Christianson, D.W.
History
DepositionMay 11, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 26, 2023Provider: repository / Type: Initial release
Revision 1.1Aug 16, 2023Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.identifier_ORCID

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Epi-isozizaene synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,8032
Polymers43,7071
Non-polymers961
Water2,900161
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)46.465, 76.156, 107.667
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

-
Components

#1: Protein Epi-isozizaene synthase / EIZS / Sesquiterpene cyclase / Sesquiterpene synthase


Mass: 43706.984 Da / Num. of mol.: 1 / Mutation: F96H
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces coelicolor A3(2) (bacteria)
Gene: cyc1, SCO5222, SC7E4.19 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9K499, epi-isozizaene synthase
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 161 / 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: 2.18 Å3/Da / Density % sol: 43.56 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop
Details: 100 mM Bis-Tris (pH 6.8), 200 mM (NH4)2SO4, 31% (w/v) PEG 3350

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.98 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Sep 24, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.99→99 Å / Num. obs: 27010 / % possible obs: 99.8 % / Redundancy: 6.5 % / Biso Wilson estimate: 25.67 Å2 / CC1/2: 0.969 / Rmerge(I) obs: 0.314 / Net I/σ(I): 13.8
Reflection shellResolution: 1.99→2.04 Å / Rmerge(I) obs: 0.801 / Mean I/σ(I) obs: 3.3 / Num. unique obs: 1857 / CC1/2: 0.551

-
Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
PHENIX1.14_3260refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.99→62.17 Å / SU ML: 0.1796 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 19.3303 / Stereochemistry target values: CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2116 1318 4.89 %
Rwork0.1835 25623 -
obs0.1849 26941 99.72 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 25.95 Å2
Refinement stepCycle: LAST / Resolution: 1.99→62.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2410 0 5 161 2576
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.012489
X-RAY DIFFRACTIONf_angle_d0.95113404
X-RAY DIFFRACTIONf_chiral_restr0.0541369
X-RAY DIFFRACTIONf_plane_restr0.0066437
X-RAY DIFFRACTIONf_dihedral_angle_d19.5949845
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.99-2.070.23571420.21312782X-RAY DIFFRACTION99.42
2.07-2.160.24791400.19342772X-RAY DIFFRACTION99.15
2.16-2.280.20851300.17512820X-RAY DIFFRACTION99.76
2.28-2.420.19791440.16922826X-RAY DIFFRACTION99.83
2.42-2.610.21881520.17012826X-RAY DIFFRACTION99.97
2.61-2.870.21641390.1792847X-RAY DIFFRACTION99.93
2.87-3.280.20711730.17912825X-RAY DIFFRACTION99.8
3.28-4.140.19791460.16922898X-RAY DIFFRACTION99.97
4.14-62.170.21631520.20613027X-RAY DIFFRACTION99.66
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)
10.923581320598-0.226174215895-0.2685365540151.044994535380.2685313611930.1528704551990.015070292890.2613571427360.0638251618851-0.237453696372-0.044867471208-0.302322292248-0.04185978349320.1795809045750.02571950091590.216113057212-0.01877330033830.03529725366910.274179250793-0.01090257791360.274581941829-2.0824842025610.0111435335-6.98569453758
20.831721546163-0.630328878125-0.3705546872291.679279229110.3683872950540.7766347416490.03829319042060.353540730506-0.278490948143-0.265631920642-0.04812311781970.0575205057676-0.1282822196050.2240840057580.01259123851310.1924258528030.0105983883171-0.004570957487740.253955299323-0.03644802394720.205685593378-1.316593271322.71889914217-2.71571058396
31.823115105541.141233043071.082939230811.599349792231.221010626681.81772969049-0.106640343590.1025011979250.152438960356-0.2105453347750.0118519374778-0.0136465202192-0.0823342671188-0.004695258898250.03461570098010.1964231976440.01272446256460.006497916844640.2062613295480.02294011774960.197753863987-6.38835880811-5.881227579-7.09670017675
40.7801501416890.2162955341980.1863007293231.78909548180.3636073166560.923099804306-0.006147235971770.0528771700632-0.06895668565690.1048921190290.01357212986710.003662774099830.1423986073750.007830575643240.003717700149390.1832164817150.0006578964699720.01148245738030.169221176640.0122609679030.183832591835-10.952643601-12.5398482634-0.925355348413
51.13512275906-0.132694978070.3666657789560.8708153095740.1896174273361.105675822430.0671598106714-0.0210863139366-0.1371606276920.04936948917660.0830988514312-0.004863513573840.01432926782460.00155654624486-0.09468557392450.165528669546-0.007897799487910.001915820879630.1709424865240.01860058545810.164111036147-18.06822625711.247516975381.91323874374
61.018536792630.3236964609770.2044114497571.185121836530.0484228279322.47998851958-0.06532420165420.213079370186-0.00856479184762-0.1360577561260.0955605855663-0.05993367276980.224359662462-0.1464786152190.002565323396830.216414016938-0.006298350514220.009166036218920.2166339315850.009175207195630.207328358897-18.8217498858.05759895114-6.65321717286
71.15949425941-0.06999013016870.9022191345141.982112350470.7289621136121.91209130521-0.09540328412660.02942140027710.147588936452-0.397205438146-0.2256834332610.239495803107-0.331066292436-0.3381019692010.2732937735680.1895651828240.02410808503220.02587492874990.2441732081820.004842282214920.230418466687-23.501042046811.8666860421-6.56544470608
81.0222418353-0.1403949567770.4390749021081.15084142346-0.5508622838332.67019955912-0.06296739864610.037559417492-0.00494657856030.00460436117277-0.0462588549154-0.07199223043750.02958402161850.1967891807750.1103227786560.1799139968430.003515419186220.01079897981780.177401837426-0.01387970787150.198931987724-8.7353340625512.97189644364.8811434282
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 17 through 51 )
2X-RAY DIFFRACTION2chain 'A' and (resid 52 through 81 )
3X-RAY DIFFRACTION3chain 'A' and (resid 82 through 107 )
4X-RAY DIFFRACTION4chain 'A' and (resid 108 through 180 )
5X-RAY DIFFRACTION5chain 'A' and (resid 181 through 222 )
6X-RAY DIFFRACTION6chain 'A' and (resid 223 through 250 )
7X-RAY DIFFRACTION7chain 'A' and (resid 251 through 301 )
8X-RAY DIFFRACTION8chain 'A' and (resid 302 through 335 )

+
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