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- PDB-6tf8: Structure of the engineered artificial aldolase I133F RA95.5-8F w... -

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Basic information

Entry
Database: PDB / ID: 6tf8
TitleStructure of the engineered artificial aldolase I133F RA95.5-8F with a bound substrate, pentan-2-one
ComponentsRA95.5-8F_133F
KeywordsLYASE / Artificial enzyme / aldolase
Biological speciesSaccharolobus solfataricus P2 (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.903 Å
AuthorsMori, T. / Macdonald, D.S.
CitationJournal: J.Am.Chem.Soc. / Year: 2020
Title: Engineered Artificial Carboligases Facilitate Regioselective Preparation of Enantioenriched Aldol Adducts.
Authors: Macdonald, D.S. / Garrabou, X. / Klaus, C. / Verez, R. / Mori, T. / Hilvert, D.
History
DepositionNov 13, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 3, 2020Provider: repository / Type: Initial release
Revision 1.1Jun 17, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.2Jan 24, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag
Revision 1.3Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: RA95.5-8F_133F
B: RA95.5-8F_133F
C: RA95.5-8F_133F
D: RA95.5-8F_133F


Theoretical massNumber of molelcules
Total (without water)116,2464
Polymers116,2464
Non-polymers00
Water8,467470
1
A: RA95.5-8F_133F


Theoretical massNumber of molelcules
Total (without water)29,0611
Polymers29,0611
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: RA95.5-8F_133F


Theoretical massNumber of molelcules
Total (without water)29,0611
Polymers29,0611
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: RA95.5-8F_133F


Theoretical massNumber of molelcules
Total (without water)29,0611
Polymers29,0611
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: RA95.5-8F_133F


Theoretical massNumber of molelcules
Total (without water)29,0611
Polymers29,0611
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)75.885, 102.316, 121.076
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
RA95.5-8F_133F


Mass: 29061.488 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharolobus solfataricus P2 (archaea)
Production host: Escherichia coli (E. coli)
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 470 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 2.02 Å3/Da / Density % sol: 39.2 %
Crystal growTemperature: 298 K / Method: evaporation, recrystallization / Details: 0.2 M NH4CL, 20% PEG3350

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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: Aug 13, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→47.324 Å / Num. obs: 73792 / % possible obs: 99.2 % / Redundancy: 6.5 % / Rmerge(I) obs: 0.096 / Net I/σ(I): 13.1
Reflection shellResolution: 1.9→2.02 Å / Redundancy: 5.35 % / Rmerge(I) obs: 0.472 / Mean I/σ(I) obs: 3.22 / Num. unique obs: 11411 / CC1/2: 0.611 / Rrim(I) all: 0.523 / % possible all: 96.1

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Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
XSCALEdata scaling
PDB_EXTRACT3.25data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5AOU

5aou


Resolution: 1.903→47.324 Å / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 23.74 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2471 2000 2.71 %
Rwork0.2 71792 -
obs0.2012 73792 99.01 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 62.8 Å2 / Biso mean: 24.8292 Å2 / Biso min: 9.63 Å2
Refinement stepCycle: final / Resolution: 1.903→47.324 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7912 0 0 470 8382
Biso mean---29.04 -
Num. residues----986
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.903-1.95060.34341310.2994470693
1.9506-2.00340.28921400.2723505899
2.0034-2.06230.32761430.24915109100
2.0623-2.12890.28311430.22795103100
2.1289-2.2050.29141420.2245115100
2.205-2.29330.25391430.2155106100
2.2933-2.39760.24431420.2139512099
2.3976-2.5240.27481420.2101512299
2.524-2.68220.21691440.2035125100
2.6822-2.88920.25751440.20625189100
2.8892-3.17990.2621440.20755170100
3.1799-3.63990.24151440.187517599
3.6399-4.58530.2151460.16195244100
4.5853-47.3240.20461520.1676545099

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