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- PDB-8of7: Cyc15 Diels Alderase -

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Basic information

Entry
Database: PDB / ID: 8of7
TitleCyc15 Diels Alderase
ComponentsRhs family protein
KeywordsLIGASE / Diels Alderase / cyclase / dimer
Function / homologyAllene oxide cyclase barrel-like domain / Allene oxide cyclase barrel like domain / antibiotic biosynthetic process / isomerase activity / GLYCINE / IMIDAZOLE / DI(HYDROXYETHYL)ETHER / SERINE / Rhs family protein
Function and homology information
Biological speciesStreptomyces sp. NL15-2K (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.66 Å
AuthorsBack, C.R. / Barringer, R.W.L. / Zorn, K. / Manzo-Ruiz, M. / Race, P.R.
Funding support United Kingdom, 4items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council (BBSRC)BB/T001968/1 United Kingdom
Biotechnology and Biological Sciences Research Council (BBSRC)BB/T008741/1 United Kingdom
Biotechnology and Biological Sciences Research Council (BBSRC)BB/L01386X/1 United Kingdom
Biotechnology and Biological Sciences Research Council (BBSRC)BB/M012107/1 United Kingdom
CitationJournal: Chembiochem / Year: 2023
Title: Interrogation of an Enzyme Library Reveals the Catalytic Plasticity of Naturally Evolved [4+2] Cyclases.
Authors: Zorn, K. / Back, C.R. / Barringer, R. / Chadimova, V. / Manzo-Ruiz, M. / Mbatha, S.Z. / Mobarec, J.C. / Williams, S.E. / van der Kamp, M.W. / Race, P.R. / Willis, C.L. / Hayes, M.A.
History
DepositionMar 14, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 21, 2023Provider: repository / Type: Initial release
Revision 1.1Jul 26, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Jun 19, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Rhs family protein
B: Rhs family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,68023
Polymers34,1362
Non-polymers1,54421
Water1,47782
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, The protein forms a dimer in solution, and during purification elutes from a size exclusion column as a dimer only.
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5120 Å2
ΔGint7 kcal/mol
Surface area12860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.140, 65.140, 180.140
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Rhs family protein


Mass: 17068.199 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces sp. NL15-2K (bacteria) / Gene: SNL152K_10620 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A401MXE6

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Non-polymers , 7 types, 103 molecules

#2: Chemical ChemComp-IMD / IMIDAZOLE


Mass: 69.085 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C3H5N2
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical
ChemComp-GLY / GLYCINE


Type: peptide linking / Mass: 75.067 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H5NO2
#6: Chemical ChemComp-SER / SERINE


Type: L-peptide linking / Mass: 105.093 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H7NO3
#7: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 82 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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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: 3.12 Å3/Da / Density % sol: 60.57 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 100 mM glutamate monohydrate, 100 mM DL-alanine, 100 mM glycine, 100 mM DL-lysine monohydrochloride, 100 mM DL-serine, 100 mM imidazole, 100 mM MES monohydrate (acid), 20 % (v/v) ethylene ...Details: 100 mM glutamate monohydrate, 100 mM DL-alanine, 100 mM glycine, 100 mM DL-lysine monohydrochloride, 100 mM DL-serine, 100 mM imidazole, 100 mM MES monohydrate (acid), 20 % (v/v) ethylene glycol, 10 % (w/v) PEG 8000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Apr 4, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.66→46.1 Å / Num. obs: 46918 / % possible obs: 100 % / Redundancy: 77.2 % / CC1/2: 0.9996 / Rmerge(I) obs: 0.101 / Net I/σ(I): 22.7
Reflection shellResolution: 1.66→1.69 Å / Num. unique obs: 2267 / CC1/2: 0.299 / % possible all: 99.65

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Processing

Software
NameVersionClassification
REFMAC5.8.0405refinement
xia2data scaling
MOLREPphasing
xia2data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.66→46.1 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.968 / SU B: 6.316 / SU ML: 0.087 / Cross valid method: THROUGHOUT / ESU R: 0.079 / ESU R Free: 0.081 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21497 2349 5 %RANDOM
Rwork0.18737 ---
obs0.18877 44470 99.91 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 60.267 Å2
Baniso -1Baniso -2Baniso -3
1-3.22 Å20 Å2-0 Å2
2--3.22 Å2-0 Å2
3----6.45 Å2
Refinement stepCycle: 1 / Resolution: 1.66→46.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2016 0 102 82 2200
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0122134
X-RAY DIFFRACTIONr_bond_other_d0.0010.0162057
X-RAY DIFFRACTIONr_angle_refined_deg1.6151.6552845
X-RAY DIFFRACTIONr_angle_other_deg0.5361.5784724
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1195253
X-RAY DIFFRACTIONr_dihedral_angle_2_deg7.714514
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.08410362
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0820.2316
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.022392
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02464
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_it3.8954.0141045
X-RAY DIFFRACTIONr_mcbond_other3.8874.011044
X-RAY DIFFRACTIONr_mcangle_it5.2427.1181287
X-RAY DIFFRACTIONr_mcangle_other5.247.1191288
X-RAY DIFFRACTIONr_scbond_it5.7724.8441089
X-RAY DIFFRACTIONr_scbond_other5.7564.8441089
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other8.1368.4851559
X-RAY DIFFRACTIONr_long_range_B_refined10.58342.282228
X-RAY DIFFRACTIONr_long_range_B_other10.58942.262226
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.66→1.703 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.507 161 -
Rwork0.506 3221 -
obs--99.56 %
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)
12.2101-0.18390.48180.8593-0.15772.9799-0.0820.01990.1545-0.01790.0345-0.0427-0.263-0.05050.04750.0335-0.0068-0.02060.01320.01650.187-27.7933-15.1197-10.2128
21.8379-0.39510.51782.8132-0.02752.6848-0.02160.3275-0.3678-0.2049-0.02220.26110.4769-0.30380.04380.1255-0.0958-0.03420.1305-0.0440.2767-32.4043-32.5645-21.3642
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A9 - 3905
2X-RAY DIFFRACTION2B9 - 2301

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