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- PDB-6yn2: Crystal structure of Renilla reniformis luciferase variant RLuc8-... -

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Basic information

Entry
Database: PDB / ID: 6yn2
TitleCrystal structure of Renilla reniformis luciferase variant RLuc8-W121F/E144Q in complex with a coelenteramide (the postcatalytic enzyme-product complex)
ComponentsCoelenterazine h 2-monooxygenase
KeywordsLUMINESCENT PROTEIN / bioluminscence / coelenteramide-bound enzyme
Function / homology
Function and homology information


Renilla-type luciferase / Renilla-luciferin 2-monooxygenase activity / carboxy-lyase activity / bioluminescence
Similarity search - Function
Epoxide hydrolase-like / alpha/beta hydrolase fold / Alpha/beta hydrolase fold-1 / Alpha/Beta hydrolase fold
Similarity search - Domain/homology
ACETATE ION / Chem-CEI / : / Coelenterazine h 2-monooxygenase
Similarity search - Component
Biological speciesRenilla reniformis (sea pansy)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.9 Å
AuthorsDamborsky, J. / Marek, M.
Funding support Czech Republic, 1items
OrganizationGrant numberCountry
European CommissionMSCA-IF-2017 792772 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
DepositionApr 10, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 21, 2021Provider: 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
Revision 1.2Jan 24, 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

Downloads & links

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Assembly

Deposited unit
A: Coelenterazine h 2-monooxygenase
B: Coelenterazine h 2-monooxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,8277
Polymers73,8142
Non-polymers1,0135
Water9,134507
1
A: Coelenterazine h 2-monooxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,3783
Polymers36,9071
Non-polymers4702
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Coelenterazine h 2-monooxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,4504
Polymers36,9071
Non-polymers5433
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)112.765, 131.077, 142.030
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Coelenterazine h 2-monooxygenase / Renilla-luciferin 2-monooxygenase / Renilla-type luciferase


Mass: 36907.156 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Renilla reniformis (sea pansy) / Production host: Escherichia coli (E. coli) / References: UniProt: P27652, Renilla-type luciferase

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Non-polymers , 5 types, 512 molecules

#2: Chemical ChemComp-CEI / N-[3-BENZYL-5-(4-HYDROXYPHENYL)PYRAZIN-2-YL]-2-(4-HYDROXYPHENYL)ACETAMIDE / COELENTERAMIDE / Coelenteramide


Mass: 411.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C25H21N3O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 507 / 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: 3.56 Å3/Da / Density % sol: 65.4 %
Crystal growTemperature: 293.5 K / Method: vapor diffusion, hanging drop / pH: 4.5 / Details: NaHPO4/K2HPO4, sodium acetate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 0.99987 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Feb 7, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99987 Å / Relative weight: 1
ReflectionResolution: 1.9→48.66 Å / Num. obs: 82701 / % possible obs: 99.9 % / Redundancy: 13.5 % / CC1/2: 0.999 / Rmerge(I) obs: 0.115 / Rpim(I) all: 0.032 / Rrim(I) all: 0.119 / Net I/σ(I): 18.5 / Num. measured all: 1120338
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
1.9-1.9412.41.844210.4950.6292.198.7
9.87-48.66120.02266810.0070.02399.2

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
XDSdata reduction
Aimless0.6.2data scaling
PHASERphasing
PHENIX1.14-3260-000refinement
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2PSJ
Resolution: 1.9→44.528 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 21.03
RfactorNum. reflection% reflection
Rfree0.1962 4176 5.05 %
Rwork0.1723 --
obs0.1735 82682 99.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 86.2 Å2 / Biso mean: 34.5373 Å2 / Biso min: 19.9 Å2
Refinement stepCycle: final / Resolution: 1.9→44.528 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5067 0 73 508 5648
Biso mean--41.32 39.96 -
Num. residues----619
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.9004-1.9220.33961200.3039252398
1.922-1.94460.28251110.26942629100
1.9446-1.96830.31511060.26032646100
1.9683-1.99330.25411620.24552552100
1.9933-2.01950.25891510.23552566100
2.0195-2.04720.24841160.23112599100
2.0472-2.07640.25241270.2232644100
2.0764-2.10740.26061360.21372595100
2.1074-2.14030.26591200.19822598100
2.1403-2.17540.21491220.19562598100
2.1754-2.21290.21211460.18362622100
2.2129-2.25320.21661410.18142593100
2.2532-2.29650.22831040.17382637100
2.2965-2.34340.17541290.17542595100
2.3434-2.39430.24631430.17682606100
2.3943-2.450.2131450.18322622100
2.45-2.51130.23431540.1812563100
2.5113-2.57920.21991590.18072605100
2.5792-2.65510.21551500.18972593100
2.6551-2.74070.23621480.18082632100
2.7407-2.83870.21771260.17912617100
2.8387-2.95230.19561580.1842613100
2.9523-3.08670.18191660.18192589100
3.0867-3.24930.19691630.18322610100
3.2493-3.45290.19921260.16692631100
3.4529-3.71930.16771510.15942649100
3.7193-4.09340.15491380.13342644100
4.0934-4.68520.1481610.12212654100
4.6852-5.90060.18791400.15022699100
5.9006-44.5280.1781570.17012782100

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