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- PDB-22ty: Crystal structure of AstC terpene cyclase domain -

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Basic information

Entry
Database: PDB / ID: 22ty
TitleCrystal structure of AstC terpene cyclase domain
ComponentsAstC
KeywordsBIOSYNTHETIC PROTEIN / haloacid dehalogenase-like terpene cyclase
Biological speciesAspergillus oryzae (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.45 Å
AuthorsChen, T.-H. / Huang, K.-F. / Ko, T.-P. / Lin, H.-C.
Funding support Taiwan, 2items
OrganizationGrant numberCountry
Academia Sinica (Taiwan)AS-CDA-109-L09 and AS-IV-114-L05 Taiwan
Ministry of Science and Technology (MoST, Taiwan)NSTC-111-2113-M-001-037-MY3 and NSTC-113-2628-M-001-014 Taiwan
CitationJournal: J.Am.Chem.Soc. / Year: 2026
Title: Dimerization-Dependent Trans-Domain Coupling Enables Intermediate Transfer in Fungal Haloacid Dehalogenase-Like Terpene Cyclases.
Authors: Chen, T.H. / Huang, K.F. / Chou, T.H. / Tseng, C.C. / Huang, R.J. / Ko, T.P. / Liang, S.Y. / Chein, R.J. / Lin, H.C.
History
DepositionJan 23, 2026Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 29, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: AstC
B: AstC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,8399
Polymers69,4212
Non-polymers4187
Water2,342130
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)160.215, 160.215, 154.315
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122
Space group name HallP612(x,y,z+5/12)
Symmetry operation#1: x,y,z
#2: x-y,x,z+1/6
#3: y,-x+y,z+5/6
#4: -y,x-y,z+1/3
#5: -x+y,-x,z+2/3
#6: x-y,-y,-z
#7: -x,-x+y,-z+2/3
#8: -x,-y,z+1/2
#9: y,x,-z+1/3
#10: -y,-x,-z+5/6
#11: -x+y,y,-z+1/2
#12: x,x-y,-z+1/6
Components on special symmetry positions
IDModelComponents
11A-637-

HOH

21B-656-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails (eV)
d_1ens_1(chain "A" and resid 200 through 501)
d_2ens_1(chain "B" and resid 200 through 501)

NCS domain segments:

Ens-ID: ens_1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_11ASPASPALAALAAA200 - 47413 - 287
d_12GOLGOLGOLGOLAC501
d_21ASPASPALAALABB200 - 47413 - 287
d_22GOLGOLGOLGOLBH501

NCS oper: (Code: givenMatrix: (-0.99838483145, -0.0568052047169, -0.00094712644428), (0.0089365047062, -0.173484054022, 0.984796132143), (-0.056105857226, 0.983197056402, 0.173711488013)Vector: 65. ...NCS oper: (Code: given
Matrix: (-0.99838483145, -0.0568052047169, -0.00094712644428), (0.0089365047062, -0.173484054022, 0.984796132143), (-0.056105857226, 0.983197056402, 0.173711488013)
Vector: 65.6456109547, 79.7479150695, -64.8904762457)

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Components

#1: Protein AstC


Mass: 34710.609 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aspergillus oryzae (mold) / Production host: Escherichia coli (E. coli)
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: Cl / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 130 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 4.12 Å3/Da / Density % sol: 70.13 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.1M sodium cacodylate trihydrate pH 6.5, 1.4M Sodium acetate trihydrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: TPS 05A / Wavelength: 1 Å
DetectorType: DECTRIS EIGER2 X 9M / Detector: PIXEL / Date: May 15, 2025
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.45→30 Å / Num. obs: 15869 / % possible obs: 100 % / Redundancy: 17.8 % / Biso Wilson estimate: 49.51 Å2 / Rmerge(I) obs: 0.357 / Net I/σ(I): 8
Reflection shellResolution: 3.45→3.57 Å / Redundancy: 16.8 % / Rmerge(I) obs: 1.326 / Mean I/σ(I) obs: 1.6 / Num. unique obs: 1550 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.45→29.71 Å / SU ML: 0.4187 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 26.9462
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2711 1363 5.01 %
Rwork0.2168 25826 -
obs0.2195 15682 93.6 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 67.26 Å2
Refinement stepCycle: LAST / Resolution: 3.45→29.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4434 0 22 145 4601
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01194559
X-RAY DIFFRACTIONf_angle_d1.30616185
X-RAY DIFFRACTIONf_chiral_restr0.0722694
X-RAY DIFFRACTIONf_plane_restr0.0099788
X-RAY DIFFRACTIONf_dihedral_angle_d13.60811664
Refine LS restraints NCSType: Torsion NCS / Rms dev position: 0.954471547789 Å
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.45-3.580.348830.30321520X-RAY DIFFRACTION55.05
3.58-3.720.31031170.29772290X-RAY DIFFRACTION83.69
3.72-3.890.33281470.24762755X-RAY DIFFRACTION99.35
3.89-4.090.26581430.22342756X-RAY DIFFRACTION99.79
4.09-4.350.2521470.20642749X-RAY DIFFRACTION99.86
4.35-4.680.23391440.18132758X-RAY DIFFRACTION99.86
4.68-5.150.31251490.20642735X-RAY DIFFRACTION99.65
5.15-5.890.34911390.2242767X-RAY DIFFRACTION99.79
5.89-7.410.23451450.2272759X-RAY DIFFRACTION99.76
7.41-29.710.2051490.17292737X-RAY DIFFRACTION99.31
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)
1-0.00230300252981-0.00159089552336-0.004612302674810.0128505206390.02200629930410.0340557534435-0.0425956354323-0.1030804179170.193170138042-0.058889885916-0.004078138032110.0536892128499-0.35782239837-0.0583593405107-0.001744400504030.750842784750.167179027698-0.1223382811961.54325624446-0.8089254661010.81195005884157.658227183888.415018784416.6959819217
20.241013415071-0.107574202520.08109163366740.1078648749470.002304593210020.0362588740319-0.0175585479463-0.4275010884180.2139924781760.1615215662660.06191172998590.0161470892309-0.04803842792250.04720225385440.1190093390810.306652863790.18467411949-0.2307568896441.36065033007-0.8948984088520.74605970062862.008168536774.711746703112.7308232208
30.00257548604463-0.01348898057810.000564809561590.1362674666120.00760872702286-0.00152999855354-0.0354583554672-0.2157574672070.1275023702940.01130517935490.121755429636-0.165782019625-0.03427309010090.0338037640834-0.0229233345413-0.1987942057780.1581120288960.1352467326010.63200630861-0.3658040960710.24893228197161.981758338367.73376326690.407831549273
41.01560947942-0.41922966162-0.004258711432630.8988580324410.03087629591440.229908284413-0.229520349221-1.09245913632-0.1126699443560.4699042652050.3819392001640.335129844492-0.0149048590771-0.3945334060250.912944075658-0.5612020399510.3831684166830.4116608994561.01568077235-0.328356402688-0.051485068800947.509671324165.35446071783.32850777728
5-0.00163668352155-0.0062129975166-0.004377985861860.461285739255-0.4672728082450.479656541516-0.0608308386059-0.5933866154370.5383498888020.166685087022-0.008916998487330.216070112049-0.226719203472-0.2584154483330.412192321171-0.1145074525190.3092411724730.2240081935330.540265079691-0.6490669335920.26977436602842.753092115577.1080554088-4.08862693443
60.283354803045-0.0203816263423-0.0457745142650.004719220456440.03733861563660.3265785509960.0255755244267-0.06474299409720.148081409759-0.04175028397950.00193328665937-0.0113023419106-0.268449887364-0.05399554917990.06348603494940.5305110485910.133639770167-0.03938961991341.06913192211-0.7806871291370.96438200328940.92121615489.57428092455.05063523897
70.209495645411-0.1058529816870.09064230563220.1448469148210.03043970090550.107739665633-0.0520743133891-0.1086892869950.21259820221-0.0575750430567-0.08109309478220.11954539675-0.0509531150969-0.0540122639579-0.1388533167480.7214180324070.2280497511210.1593107469931.10936540529-0.6817765207680.79397602626749.544626903185.842875199413.4648076807
80.2790650627090.127116887103-0.07676636082420.150184857521-0.01348371773190.158568757073-0.00677730208205-0.55876453680.2440012578070.242740677528-0.0336203146354-0.0964839823482-0.1059881333710.303731487054-0.316483026874-0.206657396502-0.0470369123789-0.0412407576751.22581167786-0.6378560530550.7884183294770.7634715005778.757665532915.877304745
91.378608589840.001284038483570.3552072341140.00541518724463-0.02449752735040.196408847522-0.06487317576760.03643692369430.5661899850790.05246317437420.0458778888158-0.00567797310228-0.1479111361970.123962835308-0.1153053759990.0599788043355-0.02030663355630.02970820583970.969045998977-0.4669008921760.5286677028881.3985229198679.00077059842.06012594962
100.2466614828920.257154648649-0.01457066088490.263713103436-0.00515027644409-0.00343328470551-0.1302982685440.3111296620060.316683990063-0.0569814815333-0.0174010303897-0.0471697625026-0.1282632055150.217314808364-0.01400213796980.077939002158-0.0693070438627-0.05516426675331.10108511942-0.3641778422770.6730629472496.6887290003374.5683091125-8.02269162768
110.0374418521791-0.007660824503580.04021412182120.0170549635411-0.0295614253690.121274417116-0.0319241564919-0.129210593559-0.04732111947580.0610902960405-0.1107481734390.08146643615240.03420420506660.246366343477-0.548227377091-0.5423477140240.02743211129730.01772399187931.1624790474-0.5409531887630.51325584275315.462154768667.69356863561.97980969333
120.289318101898-0.0481954952858-0.2420695297490.0883044083660.002344331778890.22128333402-0.1195730500820.00739747412241-0.29120823723-0.01597755595170.01315697723030.02639178411150.0770659740887-0.0808183185636-0.09585064311940.2442760664950.1666257442940.01202828546581.1710279202-0.3629901080330.74073432997923.089867933360.87128012758.77427750459
130.179320628397-0.002218297353950.05148493375430.200586861851-0.02663190682590.0164353234368-0.0690151111467-0.195023100435-0.2199037600320.03564271337060.0150414052172-0.2058920241670.03347332589680.0993311929668-0.0377377505680.2491926912730.08484353197430.09988051496591.50406065662-0.3757095626020.66771436108119.668228608469.806268366521.7019542247
140.170463965963-0.02013605792660.1471344175840.0623752104206-0.04384296630850.139858288677-0.129033955595-0.07537640373880.2893269955450.0294868270768-0.023601756903-0.0643465752087-0.05145835574010.0150823966195-0.1532845921140.273049097718-0.170399014853-0.07643341515241.53091109162-0.5797847402010.77967633815211.34834164378.574870438519.3391059269
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 200 through 229 )AA200 - 2291 - 30
22chain 'A' and (resid 230 through 271 )AA230 - 27131 - 72
33chain 'A' and (resid 272 through 298 )AA272 - 29873 - 99
44chain 'A' and (resid 299 through 363 )AA299 - 363100 - 164
55chain 'A' and (resid 364 through 399 )AA364 - 399165 - 200
66chain 'A' and (resid 400 through 432 )AA400 - 432201 - 233
77chain 'A' and (resid 433 through 474 )AA433 - 474234 - 275
88chain 'B' and (resid 200 through 259 )BG200 - 2591 - 60
99chain 'B' and (resid 260 through 285 )BG260 - 28561 - 86
1010chain 'B' and (resid 286 through 318 )BG286 - 31887 - 119
1111chain 'B' and (resid 319 through 381 )BG319 - 381120 - 182
1212chain 'B' and (resid 382 through 399 )BG382 - 399183 - 200
1313chain 'B' and (resid 400 through 432 )BG400 - 432201 - 233
1414chain 'B' and (resid 433 through 474 )BG433 - 474234 - 275

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