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- PDB-6s97: Fragment transplantation onto a hyperstable ancestor of haloalkan... -

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Basic information

Entry
Database: PDB / ID: 6s97
TitleFragment transplantation onto a hyperstable ancestor of haloalkane dehalogenases and Renilla luciferase (Anc-FT)
ComponentsFragment transplantation onto hyperstable ancestor of haloalkane dehalogenases and Renilla luciferase (Anc-FT)
KeywordsLUMINESCENT PROTEIN / fragment transplantation / ancestral enzyme / bioluminscence / coelenterazine-utilizing enzyme
Biological speciesRenilla reniformis (sea pansy)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.953 Å
AuthorsSchenkmayerova, A. / Damborsky, J. / Marek, M.
Funding support Czech Republic, 3items
OrganizationGrant numberCountry
European CommissionMSCA-IF-2017 792772 Czech Republic
Ministry of Education (Czech Republic)LQ1605, CZ.02.1.01/0.0/0.0/16_013/0001761, LM2015051, LM2015047, LM2015055 Czech Republic
European Union20776, 722610, 814418 Czech Republic
CitationJournal: Nat Commun / Year: 2021
Title: Engineering the protein dynamics of an ancestral luciferase.
Authors: Schenkmayerova, A. / Pinto, G.P. / Toul, M. / Marek, M. / Hernychova, L. / Planas-Iglesias, J. / Daniel Liskova, V. / Pluskal, D. / Vasina, M. / Emond, S. / Dorr, M. / Chaloupkova, R. / ...Authors: Schenkmayerova, A. / Pinto, G.P. / Toul, M. / Marek, M. / Hernychova, L. / Planas-Iglesias, J. / Daniel Liskova, V. / Pluskal, D. / Vasina, M. / Emond, S. / Dorr, M. / Chaloupkova, R. / Bednar, D. / Prokop, Z. / Hollfelder, F. / Bornscheuer, U.T. / Damborsky, J.
History
DepositionJul 11, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 26, 2020Provider: repository / Type: Initial release
Revision 1.1Sep 8, 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 / _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: Fragment transplantation onto hyperstable ancestor of haloalkane dehalogenases and Renilla luciferase (Anc-FT)


Theoretical massNumber of molelcules
Total (without water)33,8771
Polymers33,8771
Non-polymers00
Water2,522140
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area12080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.556, 87.556, 102.125
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein Fragment transplantation onto hyperstable ancestor of haloalkane dehalogenases and Renilla luciferase (Anc-FT)


Mass: 33877.281 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Renilla reniformis (sea pansy) / Production host: Escherichia coli #1/H766 (bacteria)
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 140 / 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: 3.34 Å3/Da / Density % sol: 63.58 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: PEG 3350, sodium acetate, Tris

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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-F / Detector: PIXEL / Date: May 12, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.95→43.78 Å / Num. obs: 33369 / % possible obs: 99.9 % / Redundancy: 20 % / CC1/2: 0.999 / Rmerge(I) obs: 0.145 / Rpim(I) all: 0.033 / Rrim(I) all: 0.149 / Net I/σ(I): 18.9
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
1.95-219.91.444599723130.8160.3251.4762.899.1
8.95-43.7817.30.035699240410.0080.03671.899.4

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation3 Å44.02 Å

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Processing

Software
NameVersionClassificationNB
PHENIX1.14_3260refinement
XDSdata reduction
Aimless0.7.4data scaling
PHASER2.8.2phasing
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.953→43.778 Å / SU ML: 0.32 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 36.43
RfactorNum. reflection% reflection
Rfree0.33 1633 4.9 %
Rwork0.2911 --
obs0.2931 33321 99.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 63.52 Å2 / Biso mean: 28.5526 Å2 / Biso min: 11.5 Å2
Refinement stepCycle: final / Resolution: 1.953→43.778 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2388 0 0 140 2528
Biso mean---32.68 -
Num. residues----294
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.9531-2.01060.36061290.2934260999
2.0106-2.07550.38221360.28582600100
2.0755-2.14970.3761400.28662575100
2.1497-2.23570.37421260.28122637100
2.2357-2.33750.35631350.29242606100
2.3375-2.46070.38071290.28362616100
2.4607-2.61490.36221280.2932643100
2.6149-2.81670.34921220.28952643100
2.8167-3.10010.31491360.29822637100
3.1001-3.54860.33551630.28122641100
3.5486-4.47010.28281390.2792688100
4.4701-43.7780.31661500.31082793100

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