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- PDB-7omr: Crystal structure of coelenteramide-bound Renilla reniformis luci... -

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Basic information

Entry
Database: PDB / ID: 7omr
TitleCrystal structure of coelenteramide-bound Renilla reniformis luciferase RLuc8-D162A variant
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 / membrane
Similarity search - Function
: / Epoxide hydrolase-like / alpha/beta hydrolase fold / Alpha/beta hydrolase fold-1 / Alpha/Beta hydrolase fold, catalytic domain / Alpha/Beta hydrolase fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-CEI / Coelenterazine h 2-monooxygenase
Similarity search - Component
Biological speciesRenilla reniformis (sea pansy)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.5 Å
AuthorsSchenkmayerova, A. / Marek, M.
Funding support Czech Republic, 1items
OrganizationGrant numberCountry
European CommissionMSCA-IF-2017 792772 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
DepositionMay 24, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 1, 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: Coelenterazine h 2-monooxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,6836
Polymers36,9031
Non-polymers7805
Water6,179343
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1550 Å2
ΔGint-8 kcal/mol
Surface area13010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.445, 74.166, 80.346
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21221

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Components

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


Mass: 36903.164 Da / Num. of mol.: 1
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
#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.: 1 / Source method: obtained synthetically / Formula: C25H21N3O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 343 / 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: 2.28 Å3/Da / Density % sol: 46.02 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: PEG8000, potassium phosphate, glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 0.9999 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Feb 7, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9999 Å / Relative weight: 1
ReflectionResolution: 1.5→46.19 Å / Num. obs: 54685 / % possible obs: 99.9 % / Redundancy: 13.1 % / CC1/2: 1 / Rmerge(I) obs: 0.09 / Rpim(I) all: 0.026 / Rrim(I) all: 0.094 / Net I/σ(I): 18.8 / Num. measured all: 717310
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
1.5-1.5311.92.1413121426260.5610.642.2371.397.6
8.22-46.19110.024444240210.0080.02580.299.7

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIX1.19.2-4158refinement
XDSdata reduction
Aimless0.6.2data scaling
PHASERphasing
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2PSJ

2psj


Resolution: 1.5→46.187 Å / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 20.44 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1861 2763 5.06 %
Rwork0.1705 51863 -
obs0.1714 54626 99.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 74.44 Å2 / Biso mean: 23.9933 Å2 / Biso min: 10.54 Å2
Refinement stepCycle: final / Resolution: 1.5→46.187 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2529 0 55 345 2929
Biso mean--36.47 33.48 -
Num. residues----309
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.5004-1.52630.33541350.3045252598
1.5263-1.5540.27251340.26172539100
1.554-1.58390.25071120.2422577100
1.5839-1.61630.26151520.23272566100
1.6163-1.65140.28151330.21982560100
1.6514-1.68980.23661270.20462583100
1.6898-1.73210.2311360.18962550100
1.7321-1.77890.19941320.19152579100
1.7789-1.83130.22731360.18842574100
1.8313-1.89040.22611370.18442574100
1.8904-1.95790.21711580.17722569100
1.9579-2.03630.22751550.17552543100
2.0363-2.1290.20341350.16872592100
2.129-2.24130.2071300.16642609100
2.2413-2.38170.16411560.16062583100
2.3817-2.56550.18581320.15792613100
2.5655-2.82370.16241220.15822644100
2.8237-3.23220.19471360.15592640100
3.2322-4.07180.12971450.14232658100
4.0718-46.1870.16951600.17012785100

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