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- PDB-22ua: Crystal structure of AstC terpene cyclase domain in complex with ... -

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Basic information

Entry
Database: PDB / ID: 22ua
TitleCrystal structure of AstC terpene cyclase domain in complex with albicanoyl monophosphate
ComponentsAstC
KeywordsBIOSYNTHETIC PROTEIN / Haloacid dehalogenase-like terpene cyclase
Function / homology:
Function and homology information
Biological speciesAspergillus oryzae (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.86 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)69,8164
Polymers69,4212
Non-polymers3942
Water2,378132
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)160.706, 160.706, 155.992
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-638-

HOH

21B-630-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails (eV)
d_1ens_1(chain "A" and resid 200 through 474)
d_2ens_1(chain "B" and resid 200 through 474)

NCS domain segments:

Component-ID: 1 / Ens-ID: ens_1 / Beg auth comp-ID: ASP / Beg label comp-ID: ASP / End auth comp-ID: ALA / End label comp-ID: ALA / Auth seq-ID: 200 - 474 / Label seq-ID: 13 - 287

Dom-IDAuth asym-IDLabel asym-ID
d_1AA
d_2BB

NCS oper: (Code: givenMatrix: (-0.998715829816, -0.050325468835, -0.0058342490381), (0.0049784645291, -0.212089793377, 0.97723750155), (-0.0504173201016, 0.975953516686, 0.212067977549)Vector: 64. ...NCS oper: (Code: given
Matrix: (-0.998715829816, -0.050325468835, -0.0058342490381), (0.0049784645291, -0.212089793377, 0.97723750155), (-0.0504173201016, 0.975953516686, 0.212067977549)
Vector: 64.9428056178, 82.9581826536, -64.8193521781)

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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.: 1 / Source method: obtained synthetically / Formula: C3H8O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-A1MEK / [(1~{S},4~{a}~{S},8~{a}~{S})-5,5,8~{a}-trimethyl-2-methylidene-3,4,4~{a},6,7,8-hexahydro-1~{H}-naphthalen-1-yl]methyl dihydrogen phosphate


Mass: 302.346 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H27O4P / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 132 / 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: 4.19 Å3/Da / Density % sol: 70.63 %
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: 2.85→30 Å / Num. obs: 28137 / % possible obs: 100 % / Redundancy: 11.9 % / Biso Wilson estimate: 51.7 Å2 / Rmerge(I) obs: 0.298 / Net I/σ(I): 14.3
Reflection shellResolution: 2.85→2.95 Å / Redundancy: 9.2 % / Rmerge(I) obs: 2.684 / Mean I/σ(I) obs: 1.8 / Num. unique obs: 2756 / % 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: 2.86→29.55 Å / SU ML: 0.3716 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 31.3103
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2883 1297 5 %
Rwork0.2582 24629 -
obs0.2597 25926 92.25 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 73.39 Å2
Refinement stepCycle: LAST / Resolution: 2.86→29.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4434 0 26 164 4624
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00534570
X-RAY DIFFRACTIONf_angle_d0.84076209
X-RAY DIFFRACTIONf_chiral_restr0.0524699
X-RAY DIFFRACTIONf_plane_restr0.0093789
X-RAY DIFFRACTIONf_dihedral_angle_d16.59881674
Refine LS restraints NCSType: Torsion NCS / Rms dev position: 1.04989600493 Å
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.86-2.970.4196730.34721385X-RAY DIFFRACTION47.63
2.97-3.110.38551300.32092470X-RAY DIFFRACTION84.83
3.11-3.270.37731490.31522834X-RAY DIFFRACTION97.68
3.27-3.470.32241530.30392910X-RAY DIFFRACTION99.48
3.47-3.740.32281550.27752935X-RAY DIFFRACTION99.77
3.74-4.120.26651550.24162944X-RAY DIFFRACTION99.9
4.12-4.710.24711550.2192969X-RAY DIFFRACTION99.97
4.71-5.930.27821590.25433009X-RAY DIFFRACTION99.84
5.93-29.550.24361680.22853173X-RAY DIFFRACTION99.85
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)
10.02022341051180.01797321179440.02759581502370.05670129519960.08010283014940.1064677240080.0445381023812-0.09043857377040.08089052413240.133299543160.020050912058-0.00031313223401-0.2321295212610.0262963361379-0.03264654635470.6387847132350.09104739362570.009971768296691.21070720595-0.7775643675610.84748566088857.814648648786.814923572914.6924509535
20.216596164716-0.006965903932450.09837262932790.08820999696760.02353281413440.0532318121817-0.0922389073959-0.3630217699990.09622356347030.1556692069370.0634294860908-0.0369149506088-0.0540968624411-0.07276347144050.03095223336820.2475194856250.202974916381-0.1317246822151.20277126875-0.6490662031340.49579689995462.41535759172.576878280911.0452533012
30.9058428499050.214533207491-0.5254181175180.0517819402535-0.121954275430.3057922643070.0239528278667-0.387477218947-0.1915672670920.158013084160.2537359981220.1748489947170.0111967319435-0.1501382645830.2850787958510.1427207060840.1522887872960.07405603149060.9760460485470.01211399538370.30609646235355.500420426960.35132941964.64419675725
40.3327609369690.0564991752848-0.1201464699970.319449716045-0.316649532550.33459354585-0.0644440298485-0.5774966226910.3655575166720.144318040350.108012489190.243021081413-0.253186906295-0.3399042280520.306512761544-0.3040731941610.4530535440790.3011070877930.812616613035-0.5612994569510.22985005611244.328515863572.5190491963-1.46182887262
50.007430364855670.0036064857013-0.01617782098540.0051267215876-0.01684927945830.0547996400669-0.0459633477348-0.161132261252-0.01186600506440.0788452017678-0.009021926794410.0377660338419-0.05744158929050.0170345665985-0.06357192398860.6512746169940.167804089320.01106012219361.24528859691-0.7541135705870.95284486160143.977854109287.176788960410.5884230568
60.04784391008940.03834947637810.009498247405460.04269743580880.003892374773530.005634719335650.0227805280087-0.02451434018470.0706784352509-0.0945640863687-0.02900092931970.0413603528445-0.0819456809915-0.001254394564990.0201394358980.7902873375540.1827523399450.1159787645040.693707530081-0.4891546949910.8387215632850.689427501588.63610850869.04106637636
70.2840296652170.0479076553754-0.0008027142268290.133238691649-0.02942016549190.007344749025890.0792933292722-0.358012273959-0.07030994414420.134537796659-0.1263327034310.00554802006188-0.03447439959550.0274235811587-0.04721399996610.158750660164-0.158877825021-0.001809405003971.16279236659-0.3959542233640.5140341847152.854530640579.096914567720.1666021553
80.1269263354070.0350503225319-0.08103728839080.0726220284617-0.07141698005330.115861390384-0.04405285375430.153446741426-0.0714357474191-0.0951094486864-0.159441034907-0.0014406957891-0.02396511861140.21245453688-0.325386608216-0.538079417789-0.0771635082899-0.03093141250461.2639966857-0.5367572229390.6257574568877.1352596287874.2563376364-0.458898438825
90.0357494196612-0.0255415124066-0.04864283957510.04464952328420.01638578056430.0763886820506-0.1321866978970.0499838956126-0.277579324599-0.0136893242086-0.0192843592010.005364857379950.09064043883560.057537275098-0.04397296937430.1776684652360.1082049770050.1269532334561.15210470857-0.1520260899840.75997136265418.310721724762.82611892197.88140272899
100.00686934556790.0195004276141-0.003230982191520.110550244373-0.02631889850690.0126464390904-0.0342943256572-0.06959260411340.01911730242880.0324775983776-0.0754480056223-0.117877064068-0.002777432662380.118090477083-0.07057354906460.236654013010.0374243757444-0.09800903171071.57025370595-0.2845037919170.60565074478616.549054501375.233363329620.2797565924
110.006037789156740.00373642102235-0.002173949003960.001466684820660.0002516992025150.0032445880645-0.0508740507444-0.0691361223053-0.1455610458850.0551079772647-0.0136541312317-0.02631149441910.1336509625560.06706231988030.0006752738324230.391955184154-0.06063620039680.05485323573291.18290757104-0.1654851150580.6578360274969.9203065179673.046688458721.2843980135
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 239 )AA200 - 2391 - 40
22chain 'A' and (resid 240 through 285 )AA240 - 28541 - 86
33chain 'A' and (resid 286 through 318 )AA286 - 31887 - 119
44chain 'A' and (resid 319 through 399 )AA319 - 399120 - 200
55chain 'A' and (resid 400 through 452 )AA400 - 452201 - 253
66chain 'A' and (resid 453 through 474 )AA453 - 474254 - 275
77chain 'B' and (resid 200 through 239 )BC200 - 2391 - 40
88chain 'B' and (resid 240 through 363 )BC240 - 36341 - 164
99chain 'B' and (resid 364 through 399 )BC364 - 399165 - 200
1010chain 'B' and (resid 400 through 452 )BC400 - 452201 - 253
1111chain 'B' and (resid 453 through 474 )BC453 - 474254 - 275

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