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- PDB-33ct: Chlororaphen Synthase from Pseudomonas chlororaphis (Pc-ChloS) in... -

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Basic information

Entry
Database: PDB / ID: 33ct
TitleChlororaphen Synthase from Pseudomonas chlororaphis (Pc-ChloS) in complex with pyrophosphate
ComponentsTerpene synthase
KeywordsLYASE / Biosynthesis / Terpenes / Type I Cyclase / C17-Precursor / Carbocation Chemistry / Catalysis
Function / homologyACETATE ION / (R,R)-2,3-BUTANEDIOL / PYROPHOSPHATE 2- / :
Function and homology information
Biological speciesPseudomonas chlororaphis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsYang, K. / Groll, M. / Dickschat, J.S.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG)GR 1861/13-1 Germany
CitationJournal: J.Am.Chem.Soc. / Year: 2026
Title: Structural Basis of Cyclized C17 Precursor Recognition and Product Formation in Chlororaphen and Grimophan Biosynthesis
Authors: Yang, K. / Groll, M. / Dickschat, J.S.
History
DepositionAug 10, 2026Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 30, 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: Terpene synthase
B: Terpene synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,82026
Polymers77,2042
Non-polymers1,61624
Water6,918384
1
A: Terpene synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,45913
Polymers38,6021
Non-polymers85712
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Terpene synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,36113
Polymers38,6021
Non-polymers75912
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)49.490, 52.600, 68.960
Angle α, β, γ (deg.)105.08, 93.26, 92.02
Int Tables number1
Space group name H-MP1

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Terpene synthase


Mass: 38601.922 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas chlororaphis (bacteria) / Gene: PchlO6_6041 / Plasmid: pETDuet-1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0AB33WV41

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Non-polymers , 8 types, 408 molecules

#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-POP / PYROPHOSPHATE 2-


Mass: 175.959 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: H2O7P2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical
ChemComp-BU3 / (R,R)-2,3-BUTANEDIOL


Mass: 90.121 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C4H10O2
#6: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C2H6O2
#7: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#8: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 384 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.24 Å3/Da / Density % sol: 45.05 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5 / Details: 0.1 M (NH4)2CO3, 0.1 M MES, 17% PEG 10000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 1.0597 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 16, 2025
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0597 Å / Relative weight: 1
ReflectionResolution: 2→30 Å / Num. obs: 42646 / % possible obs: 94.1 % / Redundancy: 3.2 % / Rmerge(I) obs: 0.096 / Net I/σ(I): 8.3
Reflection shellResolution: 2→2.1 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.763 / Mean I/σ(I) obs: 2 / Num. unique obs: 5808 / % possible all: 93.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
PDB_EXTRACTdata extraction
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→30 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.942 / SU B: 10.869 / SU ML: 0.132 / Cross valid method: THROUGHOUT / ESU R Free: 0.174 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22549 2132 5 %RANDOM
Rwork0.18198 ---
obs0.18417 40505 94.19 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 31.705 Å2
Baniso -1Baniso -2Baniso -3
1--1.44 Å21.15 Å2-0.08 Å2
2--0.01 Å2-1.34 Å2
3---1.82 Å2
Refinement stepCycle: 1 / Resolution: 2→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5142 0 97 384 5623
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0020.0135340
X-RAY DIFFRACTIONr_bond_other_d0.0010.0145036
X-RAY DIFFRACTIONr_angle_refined_deg1.111.6487238
X-RAY DIFFRACTIONr_angle_other_deg1.0981.57411527
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2685633
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.46320.209335
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.78815870
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.4821562
X-RAY DIFFRACTIONr_chiral_restr0.0460.2671
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.025964
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021288
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.8572.8462543
X-RAY DIFFRACTIONr_mcbond_other0.8562.8442540
X-RAY DIFFRACTIONr_mcangle_it1.2414.263171
X-RAY DIFFRACTIONr_mcangle_other1.2414.2613172
X-RAY DIFFRACTIONr_scbond_it0.8033.052797
X-RAY DIFFRACTIONr_scbond_other0.8033.0512798
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.1084.5014068
X-RAY DIFFRACTIONr_long_range_B_refined2.94534.0766187
X-RAY DIFFRACTIONr_long_range_B_other2.54333.6686092
X-RAY DIFFRACTIONr_rigid_bond_restr0.286310376
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.299 157 -
Rwork0.235 2975 -
obs--94.17 %
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)
10.50330.0866-0.1020.0362-0.04940.1021-0.0062-0.07250.01850.00040.00620.0112-0.02530.001700.0347-0.0054-0.00560.02850.0090.01051.4298-0.175-2.8982
20.24630.05950.05510.2280.12050.1607-0.05190.0884-0.1029-0.05130.0619-0.017-0.04530.027-0.010.0349-0.03580.01520.0496-0.03270.045417.6645-13.6587-33.1311
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A9 - 901
2X-RAY DIFFRACTION2B9 - 901

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