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- PDB-7bww: Structure of the engineered metallo-Diels-Alderase DA7 W16S -

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Basic information

Entry
Database: PDB / ID: 7bww
TitleStructure of the engineered metallo-Diels-Alderase DA7 W16S
Componentsmetallo-Diels-Alderase DA7 W16S
KeywordsDE NOVO PROTEIN / De novo Diels-Alderase
Function / homologyACETIC ACID / BENZOIC ACID / DI(HYDROXYETHYL)ETHER
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 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: PDBJ / Processing site: PDBJ
Revision 1.0Apr 21, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 10, 2021Group: Database references / Category: citation / citation_author / database_2
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 1.2Nov 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: metallo-Diels-Alderase DA7 W16S
B: metallo-Diels-Alderase DA7 W16S
C: metallo-Diels-Alderase DA7 W16S
D: metallo-Diels-Alderase DA7 W16S
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,36116
Polymers43,2244
Non-polymers1,13712
Water5,711317
1
A: metallo-Diels-Alderase DA7 W16S
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,2324
Polymers10,8061
Non-polymers4263
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area60 Å2
ΔGint-21 kcal/mol
Surface area5960 Å2
MethodPISA
2
B: metallo-Diels-Alderase DA7 W16S
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,0384
Polymers10,8061
Non-polymers2323
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area90 Å2
ΔGint-35 kcal/mol
Surface area5700 Å2
MethodPISA
3
C: metallo-Diels-Alderase DA7 W16S
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,0544
Polymers10,8061
Non-polymers2483
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area60 Å2
ΔGint-24 kcal/mol
Surface area5610 Å2
MethodPISA
4
D: metallo-Diels-Alderase DA7 W16S
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,0384
Polymers10,8061
Non-polymers2323
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area90 Å2
ΔGint-33 kcal/mol
Surface area5780 Å2
MethodPISA
5


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5060 Å2
ΔGint-160 kcal/mol
Surface area18290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)28.156, 79.823, 89.202
Angle α, β, γ (deg.)90.000, 95.570, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
metallo-Diels-Alderase DA7 W16S


Mass: 10806.048 Da / Num. of mol.: 4
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 , 6 types, 329 molecules

#2: Chemical ChemComp-BEZ / BENZOIC ACID / Benzoic acid


Mass: 122.121 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H6O2
#3: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400 / Polyethylene glycol


Mass: 238.278 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#4: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#6: Chemical ChemComp-ACY / ACETIC ACID / Acetic acid


Mass: 60.052 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H4O2
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 317 / 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: 2.31 Å3/Da / Density % sol: 46.71 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 180mM ammonium nitrate, 18% (w/v) polyethylene glycol 3350, 3% D-(+)-galactose

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 6, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.5→44.39 Å / Num. obs: 61972 / % possible obs: 98.7 % / Redundancy: 6.8 % / Biso Wilson estimate: 14.59 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.049 / Net I/σ(I): 18.9
Reflection shellResolution: 1.5→1.53 Å / Rmerge(I) obs: 0.321 / Mean I/σ(I) obs: 4.8 / Num. unique obs: 2930 / CC1/2: 0.916

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Processing

Software
NameVersionClassification
Aimlessdata scaling
PHENIX1.13_2998refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6YPI

6ypi


Resolution: 1.5→39.911 Å / SU ML: 0.15 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 20.85
RfactorNum. reflection% reflection
Rfree0.2051 2006 3.24 %
Rwork0.1881 --
obs0.1887 61880 98.55 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 69.68 Å2 / Biso mean: 21.4378 Å2 / Biso min: 7.13 Å2
Refinement stepCycle: final / Resolution: 1.5→39.911 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2805 0 64 317 3186
Biso mean--25.86 32.29 -
Num. residues----352
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.5-1.53750.23261220.2111415996
1.5375-1.57910.21421480.2009426799
1.5791-1.62560.23411520.1847429699
1.6256-1.6780.2221390.1901427299
1.678-1.7380.24861510.1936429599
1.738-1.80760.26551360.2016426599
1.8076-1.88990.24881450.2426598
1.8899-1.98950.23421450.1916426399
1.9895-2.11410.23141490.1882429799
2.1141-2.27740.19421400.186431499
2.2774-2.50650.17961450.1848428199
2.5065-2.86910.21551420.2016423197
2.8691-3.61440.20841460.1839432599
3.6144-39.9110.16381460.1759434498

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