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- PDB-7omd: Crystal structure of azacoelenterazine-bound Renilla reniformis l... -

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Basic information

Entry
Database: PDB / ID: 7omd
TitleCrystal structure of azacoelenterazine-bound Renilla reniformis luciferase variant RLuc8-D162A
ComponentsCoelenterazine h 2-monooxygenase
KeywordsLUMINESCENT PROTEIN / bioluminscence
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
DI(HYDROXYETHYL)ETHER / Chem-VK8 / Coelenterazine h 2-monooxygenase
Similarity search - Component
Biological speciesRenilla reniformis (sea pansy)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.601 Å
AuthorsSchenkmayerova, A. / Janin, Y.L. / 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 21, 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

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)75,7249
Polymers73,8062
Non-polymers1,9187
Water12,430690
1
A: Coelenterazine h 2-monooxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,5124
Polymers36,9031
Non-polymers6093
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Coelenterazine h 2-monooxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,2125
Polymers36,9031
Non-polymers1,3094
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)51.569, 84.057, 77.437
Angle α, β, γ (deg.)90.000, 90.720, 90.000
Int Tables number4
Space group name H-MP1211

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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: 36903.164 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, 697 molecules

#2: Chemical
ChemComp-VK8 / 6-(4-hydroxyphenyl)-2-[(4-hydroxyphenyl)methyl]-8-(phenylmethyl)-[1,2,4]triazolo[4,3-a]pyrazin-3-one


Mass: 424.451 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C25H20N4O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS / Feature type: SUBJECT OF INVESTIGATION / Comment: DMSO, precipitant*YM
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 690 / 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: 2 Å3/Da / Density % sol: 45.91 %
Crystal growTemperature: 293.5 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: PEG3350, Bis-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: Dec 4, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.6→43.95 Å / Num. obs: 86744 / % possible obs: 99.8 % / Redundancy: 6.7 % / CC1/2: 0.998 / Rmerge(I) obs: 0.054 / Rpim(I) all: 0.023 / Rrim(I) all: 0.059 / Net I/σ(I): 20 / Num. measured all: 585268 / Scaling rejects: 36
Reflection shell

Diffraction-ID: 1 / Redundancy: 6.4 %

Resolution (Å)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
1.6-1.631.05741700.6740.4461.15197.3
8.77-43.950.025530.9880.0110.02298.7

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
XDSdata reduction
Aimless0.7.4data scaling
PHASERphasing
PHENIX1.14-3260-000refinement
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2PSJ

2psj


Resolution: 1.601→38.401 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 21.91 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.211 4464 5.15 %
Rwork0.1761 82230 -
obs0.1778 86694 99.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 111.61 Å2 / Biso mean: 28.8524 Å2 / Biso min: 12.33 Å2
Refinement stepCycle: final / Resolution: 1.601→38.401 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5067 0 140 692 5899
Biso mean--29.93 38.25 -
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 (%)
1.601-1.61920.34761420.309265296
1.6192-1.63820.36191370.27492721100
1.6382-1.65820.28351640.26072731100
1.6582-1.67920.27631470.24252769100
1.6792-1.70130.28771470.22382695100
1.7013-1.72460.22121310.21872786100
1.7246-1.74930.21141560.21012677100
1.7493-1.77540.25121630.21232734100
1.7754-1.80310.28931500.21362722100
1.8031-1.83270.24051620.20412753100
1.8327-1.86430.27161490.20852720100
1.8643-1.89820.24921730.23222732100
1.8982-1.93470.27121590.23862740100
1.9347-1.97420.2341530.19762711100
1.9742-2.01710.23091500.19522721100
2.0171-2.0640.2381780.18862741100
2.064-2.11560.24831370.18342748100
2.1156-2.17280.2361510.18032720100
2.1728-2.23680.2271490.19162768100
2.2368-2.30890.22921330.19312720100
2.3089-2.39150.2171400.17162757100
2.3915-2.48720.1981130.17362786100
2.4872-2.60040.21961410.17462780100
2.6004-2.73740.23341730.172714100
2.7374-2.90890.21031810.17182720100
2.9089-3.13340.18851630.16772722100
3.1334-3.44850.18821400.15952788100
3.4485-3.94710.16261200.15682783100
3.9471-4.97120.16821170.1356279199
4.9712-38.4010.17391450.15872828100
Refinement TLS params.Method: refined / Origin x: 11.925 Å / Origin y: -5.64 Å / Origin z: 18.453 Å
111213212223313233
T0.0886 Å2-0.0438 Å2-0.0253 Å2-0.1681 Å2-0.0097 Å2--0.1201 Å2
L0.4112 °2-0.5161 °2-0.0302 °2-2.0175 °2-0.246 °2--0.608 °2
S0.0156 Å °-0.0253 Å °-0.0637 Å °0.0226 Å °0.0478 Å °0.1368 Å °0.0321 Å °0.009 Å °-0.047 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND ( RESID 2:310 OR RESID 401:403 OR RESID 501:854 ) ) OR ( CHAIN B AND ( RESID 404:404 OR RESID 2:311 OR RESID 401:403 OR RESID 501:836 ) )A2 - 310
2X-RAY DIFFRACTION1( CHAIN A AND ( RESID 2:310 OR RESID 401:403 OR RESID 501:854 ) ) OR ( CHAIN B AND ( RESID 404:404 OR RESID 2:311 OR RESID 401:403 OR RESID 501:836 ) )A401 - 403
3X-RAY DIFFRACTION1( CHAIN A AND ( RESID 2:310 OR RESID 401:403 OR RESID 501:854 ) ) OR ( CHAIN B AND ( RESID 404:404 OR RESID 2:311 OR RESID 401:403 OR RESID 501:836 ) )A501 - 854
4X-RAY DIFFRACTION1( CHAIN A AND ( RESID 2:310 OR RESID 401:403 OR RESID 501:854 ) ) OR ( CHAIN B AND ( RESID 404:404 OR RESID 2:311 OR RESID 401:403 OR RESID 501:836 ) )B404
5X-RAY DIFFRACTION1( CHAIN A AND ( RESID 2:310 OR RESID 401:403 OR RESID 501:854 ) ) OR ( CHAIN B AND ( RESID 404:404 OR RESID 2:311 OR RESID 401:403 OR RESID 501:836 ) )B2 - 311
6X-RAY DIFFRACTION1( CHAIN A AND ( RESID 2:310 OR RESID 401:403 OR RESID 501:854 ) ) OR ( CHAIN B AND ( RESID 404:404 OR RESID 2:311 OR RESID 401:403 OR RESID 501:836 ) )B401 - 403
7X-RAY DIFFRACTION1( CHAIN A AND ( RESID 2:310 OR RESID 401:403 OR RESID 501:854 ) ) OR ( CHAIN B AND ( RESID 404:404 OR RESID 2:311 OR RESID 401:403 OR RESID 501:836 ) )B501 - 836

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