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- PDB-7oc6: Selenomethionine derivative of alpha-humulene synthase AsR6 from ... -

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Basic information

Entry
Database: PDB / ID: 7oc6
TitleSelenomethionine derivative of alpha-humulene synthase AsR6 from Sarocladium schorii
ComponentsAlpha-humulene synthase asR6
KeywordsBIOSYNTHETIC PROTEIN / cyclase / terpene cyclase / 2E-humulene / alpha-humulene / humulene / xenovulene / tropolone sesquiterpenoid
Function / homologyalpha-humulene synthase / alpha-humulene synthase activity / terpenoid biosynthetic process / Alpha-humulene synthase asR6
Function and homology information
Biological speciesSarocladium schorii (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.01 Å
AuthorsSchotte, C. / Lukat, P. / Deuschmann, A. / Blankenfeldt, W. / Cox, R.J.
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2021
Title: Understanding and Engineering the Stereoselectivity of Humulene Synthase.
Authors: Schotte, C. / Lukat, P. / Deuschmann, A. / Blankenfeldt, W. / Cox, R.J.
History
DepositionApr 26, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 7, 2021Provider: repository / Type: Initial release
Revision 1.1Sep 15, 2021Group: Database references / Category: citation / citation_author / database_2
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Oct 23, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature
Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Alpha-humulene synthase asR6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,1516
Polymers53,7051
Non-polymers4465
Water3,027168
1
A: Alpha-humulene synthase asR6
hetero molecules

A: Alpha-humulene synthase asR6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)108,30112
Polymers107,4102
Non-polymers89110
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Buried area6310 Å2
ΔGint-116 kcal/mol
Surface area28600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)115.248, 59.117, 80.758
Angle α, β, γ (deg.)90.000, 131.520, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-1192-

HOH

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Components

#1: Protein Alpha-humulene synthase asR6 / Xenovulene A biosynthesis cluster protein R6


Mass: 53704.879 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Selenomethionine derivate of AsR6 / Source: (gene. exp.) Sarocladium schorii (fungus) / Gene: asR6 / Plasmid: pET100/D-TOPO / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A2U8U2L5, alpha-humulene synthase
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 168 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationY

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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: 1.96 Å3/Da / Density % sol: 37.4 %
Crystal growTemperature: 291 K / Method: vapor diffusion
Details: 25 % (w/v) PEG 6000, 162 mM lithium acetate, 300 mM ammonium sulfate, 5 % (v/v) glycerol, 0.1 M BIS-TRIS, Cryo: 10 % (v/v) (R,R)-2,3-butanediol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, DESY / Beamline: P11 / Wavelength: 0.9791 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 28, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2.01→57.49 Å / Num. obs: 27249 / % possible obs: 100 % / Redundancy: 13 % / Biso Wilson estimate: 33.37 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.135 / Rpim(I) all: 0.039 / Rrim(I) all: 0.14 / Net I/σ(I): 15.1 / Num. measured all: 353822 / Scaling rejects: 1
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.01-2.1212.30.8914876539580.9070.2620.932.7100
6.36-57.4911.90.084108559110.9980.0240.08744.199.9

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassification
XDSdata reduction
Aimless0.7.4data scaling
PHENIX1.19rc5refinement
PDB_EXTRACT3.27data extraction
AutoSolphasing
RefinementMethod to determine structure: SAD / Resolution: 2.01→57.49 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 20.83 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1952 1321 4.85 %
Rwork0.1646 25911 -
obs0.1661 27232 99.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 144.49 Å2 / Biso mean: 48.4788 Å2 / Biso min: 23.92 Å2
Refinement stepCycle: final / Resolution: 2.01→57.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3001 0 30 168 3199
Biso mean--65.25 43.45 -
Num. residues----381
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 9 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.01-2.090.26841390.240928833022
2.09-2.190.25011760.20628162992
2.19-2.30.2291520.186328392991
2.3-2.450.22491780.181628303008
2.45-2.630.22641540.173928643018
2.63-2.90.2088930.162329223015
2.9-3.320.18781100.170229133023
3.32-4.180.1771610.143529023063
4.18-57.490.16751580.153329423100
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)
11.79790.16161.56910.7386-0.37845.98040.03390.55410.0193-0.21610.1391-0.00480.2458-0.5541-0.16160.3277-0.0207-0.03520.5565-0.01420.3107-3.48113.48529.2453
23.7417-0.46160.00310.21150.04980.61630.0104-0.5546-0.08010.05240.00720.00080.021-0.121-0.03740.3256-0.03620.01850.30390.01690.312416.415913.229138.3494
33.8671.3996-1.07792.7875-1.39932.6201-0.03730.42930.587-0.067-0.0950.0539-0.1894-0.29670.13070.33770.0646-0.04320.31190.02280.40850.624827.667218.863
43.093-0.07130.96541.0965-0.01782.23580.10731.1660.3713-0.2389-0.1747-0.0295-0.04130.08560.02450.2930.0780.0230.51990.09980.249717.125119.48679.3233
53.5893-1.7776-0.46563.48220.98992.0490.09470.35360.0751-0.0971-0.10340.144-0.0965-0.08910.01970.26770.0227-0.00860.29560.03010.25814.048820.533321.208
66.13420.05130.26020.10770.00964.51120.04330.2142-0.2004-0.2047-0.0355-0.0618-0.0661-0.28580.00880.2631-0.0032-0.00920.24790.01930.251417.205311.664224.7084
74.4467-0.0734-0.29384.08541.13753.58570.0906-0.28450.69960.1541-0.08580.1416-0.4011-0.32350.03520.3027-0.03150.02310.2941-0.03250.384815.321521.627537.8315
82.0468-0.26010.56381.5111-0.60671.34060.02690.86140.6237-0.2186-0.1473-0.2251-0.14040.17040.0630.29330.03170.05350.44980.20430.433525.570524.78214.4146
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 5 through 25 )A5 - 25
2X-RAY DIFFRACTION2chain 'A' and (resid 26 through 86 )A26 - 86
3X-RAY DIFFRACTION3chain 'A' and (resid 87 through 123 )A87 - 123
4X-RAY DIFFRACTION4chain 'A' and (resid 124 through 198 )A124 - 198
5X-RAY DIFFRACTION5chain 'A' and (resid 199 through 244 )A199 - 244
6X-RAY DIFFRACTION6chain 'A' and (resid 245 through 292 )A245 - 292
7X-RAY DIFFRACTION7chain 'A' and (resid 293 through 327 )A293 - 327
8X-RAY DIFFRACTION8chain 'A' and (resid 328 through 391 )A328 - 391

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