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- PDB-7dvk: PyrI4 in complex with intermolecular Diels-Alder product -

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Basic information

Entry
Database: PDB / ID: 7dvk
TitlePyrI4 in complex with intermolecular Diels-Alder product
ComponentsSpiro-conjugate synthase
KeywordsISOMERASE / Diels-Alderase
Function / homologyAllene oxide cyclase barrel-like domain / Allene oxide cyclase barrel like domain / Isomerases / antibiotic biosynthetic process / isomerase activity / Chem-HOF / Spiro-conjugate synthase
Function and homology information
Biological speciesStreptomyces rugosporus (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsKashyap, R. / Addlagatta, A.
Funding support India, 3items
OrganizationGrant numberCountry
Council of Scientific & Industrial Research (CSIR)33/2018/MD-FTT&FTC-ANB India
Science and Engineering Research Board (SERB)EMR/2015/000461 India
Science and Engineering Research Board (SERB)CRG/2019/006013 India
CitationJournal: Commun Chem / Year: 2021
Title: Exo-selective intermolecular Diels-Alder reaction by PyrI4 and AbnU on non-natural substrates.
Authors: Kashyap, R. / Yerra, N.V. / Oja, J. / Bala, S. / Potuganti, R. / Thota, J.R. / Alla, M. / Pal, D. / Addlagatta, A.
History
DepositionJan 13, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 18, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Spiro-conjugate synthase
B: Spiro-conjugate synthase
C: Spiro-conjugate synthase
D: Spiro-conjugate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,91512
Polymers82,1054
Non-polymers1,8108
Water91951
1
A: Spiro-conjugate synthase
B: Spiro-conjugate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,9576
Polymers41,0522
Non-polymers9054
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3310 Å2
ΔGint-26 kcal/mol
Surface area13960 Å2
MethodPISA
2
C: Spiro-conjugate synthase
D: Spiro-conjugate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,9576
Polymers41,0522
Non-polymers9054
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3590 Å2
ΔGint-25 kcal/mol
Surface area13830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)102.959, 102.959, 168.798
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein
Spiro-conjugate synthase / [4+2] cyclase PyrI4


Mass: 20526.215 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces rugosporus (bacteria) / Gene: pyrI4 / Production host: Escherichia coli K-12 (bacteria)
References: UniProt: K7QVW7, Isomerases; Intramolecular lyases
#2: Chemical
ChemComp-HOF / methyl 4-[[(1S,6S)-6-(dimethylcarbamoyl)cyclohex-2-en-1-yl]carbamoyloxymethyl]benzoate


Mass: 360.404 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C19H24N2O5 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 51 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.72 Å3/Da / Density % sol: 54.85 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / Details: 6% Polypropylene glycol P400, 2% glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Nov 29, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.6→46.09 Å / Num. obs: 28638 / % possible obs: 99.8 % / Redundancy: 10.1 % / CC1/2: 0.999 / Rmerge(I) obs: 0.085 / Rpim(I) all: 0.028 / Rrim(I) all: 0.09 / Net I/σ(I): 20.6
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.6-2.7210.30.3563486534010.9610.1150.3756.198.7
9.01-46.048.90.03372008050.9990.0110.03542.399.1

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Processing

Software
NameVersionClassification
REFMAC5.8.0257refinement
Aimless0.7.4data scaling
PDB_EXTRACT3.27data extraction
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5BTU

5btu


Resolution: 2.6→46.022 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.88 / SU B: 10.342 / SU ML: 0.223 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.471 / ESU R Free: 0.31 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2716 1405 4.9 %RANDOM
Rwork0.2083 ---
obs0.2114 27155 99.71 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 131.09 Å2 / Biso mean: 40.918 Å2 / Biso min: 0.5 Å2
Baniso -1Baniso -2Baniso -3
1--0 Å20 Å20 Å2
2---0 Å20 Å2
3---0 Å2
Refinement stepCycle: final / Resolution: 2.6→46.022 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4840 0 134 51 5025
Biso mean--78.62 31.04 -
Num. residues----652
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0135095
X-RAY DIFFRACTIONr_bond_other_d0.0010.0174803
X-RAY DIFFRACTIONr_angle_refined_deg1.6221.6386937
X-RAY DIFFRACTIONr_angle_other_deg1.2021.5711085
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.035657
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.49221.148244
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.36815780
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.2091534
X-RAY DIFFRACTIONr_chiral_restr0.0610.2669
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.025803
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021027
LS refinement shellResolution: 2.601→2.668 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.329 90 -
Rwork0.259 1942 -
all-2032 -
obs--97.55 %

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