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- PDB-8su0: Unliganded F96H epi-Isozizaene Synthase -

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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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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

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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

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Experimental details

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Experiment

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

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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

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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

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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 )

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