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- PDB-7oc5: Alpha-humulene synthase AsR6 from Sarocladium schorii -

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Basic information

Entry
Database: PDB / ID: 7oc5
TitleAlpha-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 / MOLECULAR REPLACEMENT / molecular replacement / 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 1.2May 1, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Alpha-humulene synthase AsR6
B: Alpha-humulene synthase AsR6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,2995
Polymers97,1442
Non-polymers1553
Water6,323351
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5210 Å2
ΔGint-37 kcal/mol
Surface area29250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)121.574, 55.704, 112.045
Angle α, β, γ (deg.)90.000, 96.580, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Alpha-humulene synthase AsR6 / Xenovulene A biosynthesis cluster protein R6


Mass: 48572.062 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sarocladium schorii (fungus) / Gene: asR6 / Plasmid: pETM-11 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A2U8U2L5, alpha-humulene synthase
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 351 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 1.94 Å3/Da / Density % sol: 36.6 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.4
Details: 7.75 % (v/v) 2-propanol, 125 mM MgCl2, 25 % (w/v) PPEG 4000, 100 mM MES pH 6.4, 3 mM farnesyl pyrophosphate, Cryo: (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: 1.0332 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 11, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 2.01→111.31 Å / Num. obs: 49853 / % possible obs: 99.9 % / Redundancy: 6.6 % / Biso Wilson estimate: 25.93 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.174 / Rpim(I) all: 0.073 / Rrim(I) all: 0.189 / Net I/σ(I): 9.6 / Num. measured all: 329856 / Scaling rejects: 571
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
2.01-2.126.81.0084939372210.8320.4131.0912.799.9
6.36-111.3160.055991116580.9970.0240.0622.199.6

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIX1.19.2-4158refinement
XDSdata reduction
Aimless0.7.4data scaling
PHASERphasing
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: SAD-phased structure from deposition D_1292115439

Resolution: 2.01→60.39 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 19.61 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2004 2498 5.01 %
Rwork0.1625 47332 -
obs0.1644 49830 99.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 140.22 Å2 / Biso mean: 37.7846 Å2 / Biso min: 13.14 Å2
Refinement stepCycle: final / Resolution: 2.01→60.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5990 0 3 351 6344
Biso mean--38.96 36.05 -
Num. residues----764
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 18

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.01-2.050.25691510.21726002751100
2.05-2.090.24611180.210326382756100
2.09-2.140.24761330.204326102743100
2.14-2.190.24341490.191125872736100
2.19-2.240.22921400.177526312771100
2.24-2.30.24191400.175926232763100
2.3-2.370.19931250.167925972722100
2.37-2.450.23761510.171126122763100
2.45-2.530.22541500.169126252775100
2.53-2.630.221200.169126372757100
2.63-2.750.21221410.162826162757100
2.75-2.90.19721260.168126662792100
2.9-3.080.221480.163425842732100
3.08-3.320.20051420.162826352777100
3.32-3.650.17211400.147126282768100
3.65-4.180.15031480.134926532801100
4.18-5.270.19341450.133626522797100
5.27-60.390.18181310.17362738286999
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)
18.7744-2.8663-1.17761.44151.12513.9596-0.1968-0.3812-0.21280.03310.09460.04460.2238-0.28410.08890.2375-0.00590.04410.15710.04650.18812.474-19.35659.857
20.51760.0645-0.49520.41220.50211.7422-0.0017-0.1143-0.0840.24120.0671-0.05560.1350.2302-0.05380.2510.0088-0.01250.17870.00850.232933.509-20.24343.116
31.9742-0.2658-0.54661.0379-0.3422.87460.07450.07720.19110.1344-0.040.1021-0.1519-0.2497-0.02140.1643-0.00340.01950.1612-0.01360.237.962-10.60246.198
42.1637-0.36210.40920.96350.58775.63590.1317-0.096-0.07710.1582-0.0885-0.16270.3283-0.1657-0.11680.1844-0.00680.02090.13570.03250.22318.601-16.21647.215
53.26070.6223-0.02052.51680.59892.98520.125-0.00510.3262-0.0121-0.03990.08-0.34250.0188-0.06870.18960.02780.01330.1497-0.00030.162130.547-13.03142.477
63.4897-1.4409-0.74771.78890.14121.54170.17680.3160.5272-0.0802-0.01510.0459-0.328-0.422-0.12830.23010.05750.01770.28810.06120.263311.413-5.12632.069
70.78180.0631-1.0310.9879-0.46262.31690.01450.26180.0198-0.16120.02680.0510.0476-0.1749-0.03860.1862-0.0052-0.04190.2809-0.00870.174729.975-14.2438.075
83.34271.93033.26352.4581.62989.1093-0.15180.45260.4548-0.2360.0985-0.0328-0.91270.66870.11270.33320.0410.07790.20080.07170.403544.3820.5552.453
93.43680.0502-1.7171.37830.22233.3850.2255-0.04830.185-0.0573-0.0686-0.1194-0.25250.4281-0.13290.1356-0.0286-0.00470.2107-0.02030.185250.613-11.62418.739
102.0771-0.6571-0.14632.5417-1.55684.6-0.02220.13620.0484-0.0174-0.0153-0.0493-0.0760.02850.03470.1152-0.0181-0.01360.2155-0.0290.170140.744-12.0247.633
114.1171-2.0169-0.33086.58960.61213.2340.1410.20020.32190.01360.0264-0.1436-0.2278-0.1353-0.15250.1902-0.02540.0210.34780.0440.164826.473-10.06413.553
123.2810.5296-0.41021.0154-0.04371.34410.0977-0.15330.43970.05810.0056-0.1153-0.30770.3365-0.08080.2293-0.08150.02010.2522-0.03610.217445.123-7.2226.985
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 5:25 )A5 - 25
2X-RAY DIFFRACTION2( CHAIN A AND RESID 26:86 )A26 - 86
3X-RAY DIFFRACTION3( CHAIN A AND RESID 87:221 )A87 - 221
4X-RAY DIFFRACTION4( CHAIN A AND RESID 222:266 )A222 - 266
5X-RAY DIFFRACTION5( CHAIN A AND RESID 267:327 )A267 - 327
6X-RAY DIFFRACTION6( CHAIN A AND RESID 328:393 )A328 - 393
7X-RAY DIFFRACTION7( CHAIN B AND RESID 5:86 )B5 - 86
8X-RAY DIFFRACTION8( CHAIN B AND RESID 87:123 )B87 - 123
9X-RAY DIFFRACTION9( CHAIN B AND RESID 124:198 )B124 - 198
10X-RAY DIFFRACTION10( CHAIN B AND RESID 199:266 )B199 - 266
11X-RAY DIFFRACTION11( CHAIN B AND RESID 267:327 )B267 - 327
12X-RAY DIFFRACTION12( CHAIN B AND RESID 328:392 )B328 - 392

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