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- PDB-6tfa: Structure of the engineered retro-aldolase RA95.5-8F F112L -

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Basic information

Entry
Database: PDB / ID: 6tfa
TitleStructure of the engineered retro-aldolase RA95.5-8F F112L
ComponentsF112L RA95.5-8F
KeywordsLYASE / artificial enzyme / aldolase
Function / homologyAldolase class I / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Function and homology information
Biological speciesSaccharolobus solfataricus P2 (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.163 Å
AuthorsKlaus, C. / Macdonald, D.S. / Hilvert, D.
Funding support Switzerland, 1items
OrganizationGrant numberCountry
Swiss National Science Foundation Switzerland
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 / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: F112L RA95.5-8F
B: F112L RA95.5-8F
C: F112L RA95.5-8F
D: F112L RA95.5-8F


Theoretical massNumber of molelcules
Total (without water)119,5464
Polymers119,5464
Non-polymers00
Water2,648147
1
A: F112L RA95.5-8F


Theoretical massNumber of molelcules
Total (without water)29,8861
Polymers29,8861
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: F112L RA95.5-8F


Theoretical massNumber of molelcules
Total (without water)29,8861
Polymers29,8861
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: F112L RA95.5-8F


Theoretical massNumber of molelcules
Total (without water)29,8861
Polymers29,8861
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: F112L RA95.5-8F


Theoretical massNumber of molelcules
Total (without water)29,8861
Polymers29,8861
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)75.098, 101.865, 120.527
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
F112L RA95.5-8F


Mass: 29886.414 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharolobus solfataricus P2 (archaea)
Production host: Escherichia coli BL21(DE3) (bacteria)
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 147 / Source method: isolated from a natural source / Formula: H2O

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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: 2.03 Å3/Da / Density % sol: 39.43 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 6.14
Details: 200 mM sodium chloride 22.91 %w/v PEG 3350 100 mM BIS-TRIS pH 6.14

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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 4, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.16→49.92 Å / Num. obs: 49820 / % possible obs: 99.44 % / Redundancy: 6 % / Rmerge(I) obs: 0.177 / Net I/σ(I): 5.7
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
2.16-2.235.42.4472260741640.381.1092.6971.397.5
8.92-4760.12849968270.9770.0560.1413.899.4

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation2.87 Å47 Å
Translation2.87 Å47 Å

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Processing

Software
NameVersionClassificationNB
PHENIX1.16_3549refinement
XDSdata reduction
Aimless0.7.4data scaling
PHASER2.8.1phasing
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5AN7

5an7


Resolution: 2.163→47.001 Å / SU ML: 0.27 / Cross valid method: THROUGHOUT / σ(F): 0.97 / Phase error: 31.27
RfactorNum. reflection% reflection
Rfree0.2785 1999 4.01 %
Rwork0.2285 --
obs0.2304 49820 99.44 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 86.43 Å2 / Biso mean: 46.3669 Å2 / Biso min: 24.86 Å2
Refinement stepCycle: final / Resolution: 2.163→47.001 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7629 0 0 147 7776
Biso mean---43.05 -
Num. residues----974
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.163-2.2170.34011380.3201330397
2.217-2.27690.37221410.30463356100
2.2769-2.34390.33771400.29763364100
2.3439-2.41960.3261410.29533397100
2.4196-2.50610.31451410.27483373100
2.5061-2.60640.27911410.27433384100
2.6064-2.7250.32561430.26323409100
2.725-2.86860.30491430.2753417100
2.8686-3.04830.29181410.25533390100
3.0483-3.28370.31171450.24323434100
3.2837-3.6140.30631420.2292342699
3.614-4.13670.28421450.2006345299
4.1367-5.21070.23931460.1743347099
5.2107-47.0010.2141520.1944364699

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