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- PDB-7qxq: Coelenteramide-bound Renilla-type luciferase (AncFT) -

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Basic information

Entry
Database: PDB / ID: 7qxq
TitleCoelenteramide-bound Renilla-type luciferase (AncFT)
ComponentsFragment transplantation onto hyperstable ancestor of haloalkane dehalogenases and Renilla luciferase (Anc-FT)
KeywordsOXIDOREDUCTASE / luciferase / coelenteramide / Renilla-like / engineered ancestor
Function / homologyAlpha/Beta hydrolase fold, catalytic domain / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta / Chem-CEI
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.251 Å
AuthorsMarek, M. / Schenkmayerova, A.
Funding support Czech Republic, 1items
OrganizationGrant numberCountry
Czech Science Foundation22-09853S Czech Republic
CitationJournal: Nat Catal / Year: 2023
Title: Catalytic mechanism for Renilla-type luciferases
Authors: Schenkmayerova, A. / Toul, M. / Pluskal, D. / Baatallah, R. / Gagnot, G. / Pinto, G.P. / Santana, V.T. / Stuchla, M. / Neugebauer, P. / Chaiyen, P. / Damborsky, J. / Bednar, D. / Janin, Y.L. ...Authors: Schenkmayerova, A. / Toul, M. / Pluskal, D. / Baatallah, R. / Gagnot, G. / Pinto, G.P. / Santana, V.T. / Stuchla, M. / Neugebauer, P. / Chaiyen, P. / Damborsky, J. / Bednar, D. / Janin, Y.L. / Prokop, Z. / Marek, M.
History
DepositionJan 27, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 7, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 18, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Jan 31, 2024Group: 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: Fragment transplantation onto hyperstable ancestor of haloalkane dehalogenases and Renilla luciferase (Anc-FT)
B: Fragment transplantation onto hyperstable ancestor of haloalkane dehalogenases and Renilla luciferase (Anc-FT)
C: Fragment transplantation onto hyperstable ancestor of haloalkane dehalogenases and Renilla luciferase (Anc-FT)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)109,1946
Polymers107,9603
Non-polymers1,2343
Water4,954275
1
A: Fragment transplantation onto hyperstable ancestor of haloalkane dehalogenases and Renilla luciferase (Anc-FT)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,3982
Polymers35,9871
Non-polymers4111
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Fragment transplantation onto hyperstable ancestor of haloalkane dehalogenases and Renilla luciferase (Anc-FT)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,3982
Polymers35,9871
Non-polymers4111
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Fragment transplantation onto hyperstable ancestor of haloalkane dehalogenases and Renilla luciferase (Anc-FT)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,3982
Polymers35,9871
Non-polymers4111
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)49.224, 83.332, 102.017
Angle α, β, γ (deg.)90.000, 91.890, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 35986.590 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli) / References: Renilla-type luciferase
#2: Chemical ChemComp-CEI / N-[3-BENZYL-5-(4-HYDROXYPHENYL)PYRAZIN-2-YL]-2-(4-HYDROXYPHENYL)ACETAMIDE / COELENTERAMIDE


Mass: 411.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C25H21N3O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 275 / Source method: isolated from a natural source / Formula: H2O
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: 1.97 Å3/Da / Density % sol: 37.61 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: magnesium acetate, PEG 3350

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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: 1.8→44.9 Å / Num. obs: 75744 / % possible obs: 99.3 % / Redundancy: 6.7 % / CC1/2: 0.997 / Net I/σ(I): 10.9
Reflection shellResolution: 1.8→1.84 Å / Num. unique obs: 4404 / CC1/2: 0.594

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
XDSdata reduction
Aimlessdata scaling
PHASERphasing
PHENIX1.14_3260refinement
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6S97

6s97


Resolution: 2.251→44.891 Å / SU ML: 0.26 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 25.59 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2408 1920 4.93 %
Rwork0.1715 37060 -
obs0.1749 38980 99.55 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 83.76 Å2 / Biso mean: 29.9928 Å2 / Biso min: 9.56 Å2
Refinement stepCycle: final / Resolution: 2.251→44.891 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7230 0 93 275 7598
Biso mean--36.45 29.67 -
Num. residues----888
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.251-2.30680.351310.2434253298
2.3068-2.36920.30641160.1912676100
2.3692-2.43890.29391360.17892655100
2.4389-2.51760.25521470.17872602100
2.5176-2.60760.27991500.18312657100
2.6076-2.7120.27611180.19422655100
2.712-2.83540.27871410.18272630100
2.8354-2.98480.2861160.19072655100
2.9848-3.17180.26021510.18642648100
3.1718-3.41660.24481390.17012646100
3.4166-3.76030.22591370.173267399
3.7603-4.3040.22151280.1517263899
4.304-5.42110.19441390.13722703100
5.4211-44.8910.1891710.16272690100

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