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- PDB-6ypi: Structure of the engineered metallo-Diels-Alderase DA7 W16G,K58Q,... -

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Entry
Database: PDB / ID: 6ypi
TitleStructure of the engineered metallo-Diels-Alderase DA7 W16G,K58Q,L77R,T78R
ComponentsDA7 W16G,K58Q,L77R,T78R
KeywordsDE NOVO PROTEIN / De novo Diels-Alderase
Function / homologyBENZOIC ACID / 3-[BENZYL(DIMETHYL)AMMONIO]PROPANE-1-SULFONATE / DI(HYDROXYETHYL)ETHER
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.479 Å
AuthorsBasler, S. / Mori, T. / Hilvert, D.
CitationJournal: Nat.Chem. / Year: 2021
Title: Efficient Lewis acid catalysis of an abiological reaction in a de novo protein scaffold.
Authors: Basler, S. / Studer, S. / Zou, Y. / Mori, T. / Ota, Y. / Camus, A. / Bunzel, H.A. / Helgeson, R.C. / Houk, K.N. / Jimenez-Oses, G. / Hilvert, D.
History
DepositionApr 16, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 28, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 10, 2021Group: Data collection / Database references
Category: citation / citation_author ...citation / citation_author / database_2 / pdbx_database_proc
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Jun 19, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DA7 W16G,K58Q,L77R,T78R
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,4265
Polymers10,8751
Non-polymers5514
Water59433
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1100 Å2
ΔGint-24 kcal/mol
Surface area5820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.237, 35.015, 43.229
Angle α, β, γ (deg.)90.000, 109.810, 90.000
Int Tables number5
Space group name H-MC121

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Components

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Protein , 1 types, 1 molecules A

#1: Protein DA7 W16G,K58Q,L77R,T78R


Mass: 10875.097 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli)

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Non-polymers , 5 types, 37 molecules

#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#4: Chemical ChemComp-DMX / 3-[BENZYL(DIMETHYL)AMMONIO]PROPANE-1-SULFONATE


Mass: 257.349 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H19NO3S
#5: Chemical ChemComp-BEZ / BENZOIC ACID


Mass: 122.121 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H6O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 33 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.04 Å3/Da / Density % sol: 39.63 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 100 mM HEPES pH 7.5, 2 M (NH4)2SO4, 2% (w/v) polyethylene glycol 400, and 100 mM NDSB-256

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Oct 7, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.479→40.67 Å / Num. obs: 14704 / % possible obs: 99.5 % / Redundancy: 3.3 % / Biso Wilson estimate: 23.54 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.025 / Net I/σ(I): 12.1
Reflection shellResolution: 1.48→1.51 Å / Rmerge(I) obs: 0.722 / Mean I/σ(I) obs: 0.9 / Num. unique obs: 717 / CC1/2: 0.61

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
Aimlessdata scaling
PDB_EXTRACT3.25data extraction
XDSdata reduction
AutoSolphasing
RefinementMethod to determine structure: SAD / Resolution: 1.479→40.669 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 29.96 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflection
Rfree0.2296 735 5 %
Rwork0.2069 13963 -
obs0.208 14698 99.31 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 82.28 Å2 / Biso mean: 29.3173 Å2 / Biso min: 17.33 Å2
Refinement stepCycle: final / Resolution: 1.479→40.669 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms701 0 51 33 785
Biso mean--33.98 36.85 -
Num. residues----87
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.4794-1.59360.33591460.3014276799
1.5936-1.7540.30991460.2351277599
1.754-2.00780.22031450.2003276499
2.0078-2.52960.22491480.20892813100
2.5296-40.6690.2181500.1975284499

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