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- PDB-7oc4: Alpha-humulene synthase AsR6 from Sarocladium schorii in complex ... -

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Basic information

Entry
Database: PDB / ID: 7oc4
TitleAlpha-humulene synthase AsR6 from Sarocladium schorii in complex with thiolodiphosphate and a cyclized reaction product.
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 / (R,R)-2,3-BUTANEDIOL / TRIHYDROGEN THIODIPHOSPHATE / Chem-V8Z / Alpha-humulene synthase asR6
Function and homology information
Biological speciesSarocladium schorii (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.03 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

Downloads & links

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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)98,50116
Polymers97,1442
Non-polymers1,35714
Water7,458414
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7200 Å2
ΔGint-77 kcal/mol
Surface area28320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.911, 64.256, 86.508
Angle α, β, γ (deg.)90.000, 101.230, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 2 molecules AB

#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

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Non-polymers , 7 types, 428 molecules

#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-PIS / TRIHYDROGEN THIODIPHOSPHATE / THIOPYROPHOSPHATE


Mass: 193.033 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: H3O6P2S / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-BU3 / (R,R)-2,3-BUTANEDIOL


Mass: 90.121 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O2
#5: Chemical ChemComp-V8Z / (1E,4E,8E)-2,6,6,9-Tetramethyl-1,4-8-cycloundecatriene / (1E,8E)-2,6,6,9-tetramethylcycloundeca-1,4,8-triene / 134687947 / alpha-Caryophyllene / 3,7,10-Humulatriene


Mass: 204.351 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H24
#6: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#7: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 414 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.07 Å3/Da / Density % sol: 40.7 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.4
Details: 15.25 % (v/v) ethanol, 88 mM Mg acetate, 23 % (w/v) PEG 2000 MME, 4 % PEG 200, 100 mM MES pH 6.4, 3 mM farnesyl thiopyrophosphate, 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: 1.0332 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 13, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 2.03→72.5 Å / Num. obs: 51626 / % possible obs: 99.7 % / Redundancy: 6.7 % / Biso Wilson estimate: 26.94 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.131 / Rpim(I) all: 0.054 / Rrim(I) all: 0.142 / Net I/σ(I): 9.6 / Num. measured all: 344665
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
2.03-2.146.80.7615095974540.8610.3120.8232.599.4
6.41-72.56.10.0461044017070.9980.020.0526.899.6

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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: 2.03→51.23 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 19.66 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1875 1251 2.42 %
Rwork0.1557 50343 -
obs0.1565 51594 99.59 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 158.68 Å2 / Biso mean: 38.6334 Å2 / Biso min: 16.7 Å2
Refinement stepCycle: final / Resolution: 2.03→51.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6142 0 140 414 6696
Biso mean--45.33 37.52 -
Num. residues----775
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.03-2.110.29041380.22935548568699
2.11-2.20.23341360.19195509564599
2.21-2.320.20541400.17165575571599
2.32-2.470.22261380.164955725710100
2.47-2.660.18491380.161455405678100
2.66-2.920.20991390.154756145753100
2.92-3.350.19991390.150856225761100
3.35-4.220.14971400.128356195759100
4.22-51.230.16221430.15257445887100
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)
10.15880.1473-0.13450.1495-0.07450.25010.0189-0.45570.01460.46380.0116-0.0321-0.0692-0.084400.39220.02160.01230.32760.00060.2283-24.6519.889-15.819
20.2222-0.0152-0.10050.0858-0.06360.08640.0110.12520.1424-0.03830.07420.0776-0.0313-0.1252-00.2888-0.00870.00430.29340.00980.3495-24.40222.531-50.893
30.78910.2729-0.17640.78610.16510.8524-0.0346-0.1591-0.06370.04420.06790.22750.0245-0.110100.30040.01340.01670.27220.0370.3305-28.6346.411-26.773
40.7899-0.39230.31110.80010.39980.90040.0059-0.1539-0.0350.1599-0.0394-0.0387-0.04210.0615-00.2180.0044-0.00020.19360.00190.2246-8.39212.661-27.624
50.7471-0.0471-0.32550.6568-0.15381.19390.03130.01370.05380.06230.0506-0.0089-0.0572-0.0292-00.18520.02030.0130.19290.00010.2358-19.88218.198-35.569
60.4621-0.12840.06110.7120.29010.7468-0.0147-0.0277-0.02550.04330.06290.09420.019-0.0943-00.2084-0.01930.00580.19810.01130.2356-20.81615.31-48.296
70.7101-0.0467-0.14240.682-0.10530.6031-0.0735-0.1191-0.04550.09980.0076-0.10620.1140.2847-00.25240.0522-0.00930.26830.02220.2942-1.9751.416-31.677
80.02920.0526-0.00210.16110.13380.26520.20810.2606-0.0646-0.2268-0.1809-0.03530.16670.9547-00.45870.0234-0.02440.61990.01270.32177.98617.251-89.225
90.4721-0.21860.32250.3337-0.3330.3687-0.07290.26330.0546-0.1570.0643-0.12070.0750.289200.3097-0.0109-0.00930.3818-0.00820.39488.62216.599-53.549
101.57990.4136-0.1480.8780.06162.71730.01950.27-0.2155-0.16820.0198-0.09650.22360.21320.00040.31860.0126-0.02460.2925-0.02120.283-3.22311.29-77.835
111.5490.79120.0480.42460.09462.080.33620.2532-0.074-0.1687-0.1567-0.5330.25790.3235-00.34480.0098-0.05040.3382-0.0050.3793.93214.962-68.704
120.8764-0.35320.23240.70010.61291.0346-0.23340.3972-0.2368-0.33620.235-0.26360.2095-0.10380.00010.3057-0.0161-0.00070.3011-0.00260.32361.13312.977-60.237
130.8653-0.285-0.13310.18810.01370.8962-0.0885-0.1173-0.2472-0.05820.12280.17550.19080.105500.24720.00440.01020.26430.01650.30757.1998.184-52.711
140.5572-0.48990.08590.69290.05261.37720.02440.1973-0.0793-0.1363-0.01030.1690.2415-0.2196-00.2792-0.0422-0.01040.3105-0.00710.2656-15.15210.074-68.766
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 87:123 )A87 - 123
4X-RAY DIFFRACTION4( CHAIN A AND RESID 124:198 )A124 - 198
5X-RAY DIFFRACTION5( CHAIN A AND RESID 199:292 )A199 - 292
6X-RAY DIFFRACTION6( CHAIN A AND RESID 293:347 )A293 - 347
7X-RAY DIFFRACTION7( CHAIN A AND RESID 348:393 )A348 - 393
8X-RAY DIFFRACTION8( CHAIN B AND RESID 4:25 )B4 - 25
9X-RAY DIFFRACTION9( CHAIN B AND RESID 26:86 )B26 - 86
10X-RAY DIFFRACTION10( CHAIN B AND RESID 87:221 )B87 - 221
11X-RAY DIFFRACTION11( CHAIN B AND RESID 222:266 )B222 - 266
12X-RAY DIFFRACTION12( CHAIN B AND RESID 267:296 )B267 - 296
13X-RAY DIFFRACTION13( CHAIN B AND RESID 297:327 )B297 - 327
14X-RAY DIFFRACTION14( CHAIN B AND RESID 328:392 )B328 - 392

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