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

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Basic information

Entry
Database: PDB / ID: 33cv
TitleChlororaphen Synthase from Pseudomonas chlororaphis (Pc-ChloS) in complex with prechlororaphen thiolopyrophosphate (a-PCSPP)
ComponentsChloS
KeywordsLYASE / Biosynthesis / Terpenes / Type I Cyclase / C17-Precursor / Carbocation Chemistry / Catalysis
Function / homology: / ACETATE ION / (R,R)-2,3-BUTANEDIOL / DI(HYDROXYETHYL)ETHER
Function and homology information
Biological speciesPseudomonas chlororaphis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 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
Revision 1.1Nov 4, 2026Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ChloS
B: ChloS
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,15323
Polymers77,2042
Non-polymers1,94921
Water3,909217
1
A: ChloS
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,59911
Polymers38,6021
Non-polymers99710
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: ChloS
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,55412
Polymers38,6021
Non-polymers95211
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)49.150, 52.290, 71.210
Angle α, β, γ (deg.)105.25, 101.22, 93.39
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 ChloS


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

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Non-polymers , 9 types, 238 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-A1KN5 / Prechlororaphen thiolopyrophosphate / [(~{E})-5-[(1~{S},4~{R},5~{R})-3-ethyl-1,2,4,5-tetramethyl-cyclopent-2-en-1-yl]-3-methyl-pent-2-enyl]sulfanyl-phosphonooxy-phosphinic acid


Mass: 426.445 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H32O6P2S / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#5: Chemical ChemComp-BU3 / (R,R)-2,3-BUTANEDIOL


Mass: 90.121 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H10O2
#6: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 5 / 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-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#9: Chemical ChemComp-NA / SODIUM ION


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


Mass: 18.015 Da / Num. of mol.: 217 / 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: 2.23 Å3/Da / Density % sol: 44.79 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.2 / Details: 1 M Na/K-phosphate

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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: 0.9393 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: May 3, 2026
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9393 Å / Relative weight: 1
ReflectionResolution: 1.9→30 Å / Num. obs: 51470 / % possible obs: 97.9 % / Redundancy: 5.2 % / Rmerge(I) obs: 0.106 / Net I/σ(I): 8.5
Reflection shellResolution: 1.9→2 Å / Redundancy: 5.3 % / Rmerge(I) obs: 0.824 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 7235 / % possible all: 96.2

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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: 1.9→30 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.934 / SU B: 9.7 / SU ML: 0.121 / Cross valid method: THROUGHOUT / ESU R Free: 0.148 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22221 2573 5 %RANDOM
Rwork0.18371 ---
obs0.18595 48882 97.93 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 30.032 Å2
Baniso -1Baniso -2Baniso -3
1--1.27 Å20.22 Å2-1.5 Å2
2--1.14 Å2-0.17 Å2
3---0.69 Å2
Refinement stepCycle: 1 / Resolution: 1.9→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5129 0 103 217 5449
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0030.0135337
X-RAY DIFFRACTIONr_bond_other_d0.0010.0145038
X-RAY DIFFRACTIONr_angle_refined_deg1.2611.6547238
X-RAY DIFFRACTIONr_angle_other_deg1.1741.58311533
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7275631
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.98420.18334
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.48615870
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.891562
X-RAY DIFFRACTIONr_chiral_restr0.0580.2672
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.025956
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_it1.2562.8042536
X-RAY DIFFRACTIONr_mcbond_other1.2552.8012532
X-RAY DIFFRACTIONr_mcangle_it1.7844.1953161
X-RAY DIFFRACTIONr_mcangle_other1.7844.1963162
X-RAY DIFFRACTIONr_scbond_it1.1933.0752801
X-RAY DIFFRACTIONr_scbond_other1.1933.0762802
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.6144.5134078
X-RAY DIFFRACTIONr_long_range_B_refined2.71432.9856147
X-RAY DIFFRACTIONr_long_range_B_other2.65432.9216110
X-RAY DIFFRACTIONr_rigid_bond_restr0.451310375
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.381 184 -
Rwork0.331 3488 -
obs--95.06 %
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)
10.29730.011-0.06270.08250.00850.1094-0.0046-0.04030.02320.01530.00610.0031-0.0161-0.0012-0.00150.02070.0025-0.00350.00850.00130.02161.4718-0.2755-2.8875
20.283-0.0283-0.00940.0945-0.00140.06870.00110.0569-0.0371-0.0333-0.0042-0.00790.017-0.00230.00310.0199-0.00670.00430.0213-0.00680.01817.6975-13.8496-33.0239
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A10 - 901
2X-RAY DIFFRACTION2B11 - 901

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