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- PDB-7dvi: Crystal Structure of AbnU: An exo-specific intermolecular Diels-A... -

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Basic information

Entry
Database: PDB / ID: 7dvi
TitleCrystal Structure of AbnU: An exo-specific intermolecular Diels-Alderase
ComponentsAOC_like domain-containing protein
KeywordsISOMERASE / Diels ALderase
Function / homologyAllene oxide cyclase barrel-like domain / Allene oxide cyclase barrel like domain / antibiotic biosynthetic process / isomerase activity / AOC_like domain-containing protein
Function and homology information
Biological speciesFrankia sp. Cc1.17 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2 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: AOC_like domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,45323
Polymers17,0721
Non-polymers1,38222
Water1,24369
1
A: AOC_like domain-containing protein
hetero molecules

A: AOC_like domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,90746
Polymers34,1442
Non-polymers2,76344
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation9_555-x,-x+y,-z+2/31
Unit cell
Length a, b, c (Å)104.437, 104.437, 67.661
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number181
Space group name H-MP6422
Components on special symmetry positions
IDModelComponents
11A-369-

HOH

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Components

#1: Protein AOC_like domain-containing protein


Mass: 17071.918 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Frankia sp. Cc1.17 (bacteria) / Gene: CC117_14200 / Production host: Escherichia coli K-12 (bacteria) / References: UniProt: A0A1S1R073
#2: Chemical...
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 21 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 69 / Source method: isolated from a natural source / Formula: H2O
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: 298 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 1 M Imidazole, pH 7.0, 20% Ethanol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 11.2C / Wavelength: 0.974 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: May 28, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.974 Å / Relative weight: 1
ReflectionResolution: 2→45.26 Å / Num. obs: 15158 / % possible obs: 99.9 % / Redundancy: 36.4 % / CC1/2: 1 / Rmerge(I) obs: 0.064 / Rpim(I) all: 0.011 / Rrim(I) all: 0.065 / Net I/σ(I): 40.6
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
2-2.0534.30.6293743010920.9760.1080.6387.698.8
8.96-45.22260.03557762220.9990.0070.03590.499.3

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Phasing

PhasingMethod: molecular replacement

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Processing

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

5dyv


Resolution: 2→45.22 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.942 / SU B: 3.591 / SU ML: 0.097 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.143 / ESU R Free: 0.147 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.244 724 4.8 %RANDOM
Rwork0.1908 ---
obs0.1932 14411 99.89 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 91.81 Å2 / Biso mean: 36.25 Å2 / Biso min: 22.22 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å2-0 Å2
3----0.01 Å2
Refinement stepCycle: final / Resolution: 2→45.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1075 0 92 69 1236
Biso mean--56.88 46.13 -
Num. residues----134
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0131203
X-RAY DIFFRACTIONr_bond_other_d0.0010.0171134
X-RAY DIFFRACTIONr_angle_refined_deg1.7641.6771590
X-RAY DIFFRACTIONr_angle_other_deg1.3261.5762604
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.9815141
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.63321.06775
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.04515181
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.1381512
X-RAY DIFFRACTIONr_chiral_restr0.090.2133
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.021322
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02270
LS refinement shellResolution: 2.003→2.055 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.333 63 -
Rwork0.255 1028 -
all-1091 -
obs--98.91 %

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