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- PDB-7omo: Crystal structure of coelenteramine-bound Renilla reniformis luci... -

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Basic information

Entry
Database: PDB / ID: 7omo
TitleCrystal structure of coelenteramine-bound Renilla reniformis luciferase RLuc8-D120A variant
ComponentsRenilla reniformis luciferase RLuc8-D120A variant
KeywordsLUMINESCENT PROTEIN / bioluminscence / coelenteramide-bound enzyme
Function / homologyAlpha/Beta hydrolase fold, catalytic domain / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta / 4-[5-azanyl-6-(phenylmethyl)pyrazin-2-yl]phenol
Function and homology information
Biological speciesRenilla reniformis (sea pansy)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.451 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 1.2Jun 19, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Renilla reniformis luciferase RLuc8-D120A variant
B: Renilla reniformis luciferase RLuc8-D120A variant
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,57211
Polymers73,8062
Non-polymers7659
Water8,341463
1
A: Renilla reniformis luciferase RLuc8-D120A variant
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,5418
Polymers36,9031
Non-polymers6387
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Renilla reniformis luciferase RLuc8-D120A variant
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,0313
Polymers36,9031
Non-polymers1282
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)49.315, 139.972, 50.623
Angle α, β, γ (deg.)90.000, 112.560, 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 Renilla reniformis luciferase RLuc8-D120A variant


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)

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Non-polymers , 5 types, 472 molecules

#2: Chemical ChemComp-VKB / 4-[5-azanyl-6-(phenylmethyl)pyrazin-2-yl]phenol


Mass: 277.321 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H15N3O / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3 / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 463 / 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: 43.74 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: PEG3350, magnesium chloride, bis-tris

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 0.999 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Aug 27, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.999 Å / Relative weight: 1
ReflectionResolution: 1.45→46.751 Å / Num. obs: 111521 / % possible obs: 99.9 % / Redundancy: 6.8 % / Biso Wilson estimate: 17.13 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.046 / Rpim(I) all: 0.019 / Rrim(I) all: 0.049 / Net I/σ(I): 21.2
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
1.45-1.486.80.86154150.8070.3530.93299.2
7.95-106.40.0227080.9990.0110.02499.8

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Phasing

PhasingMethod: molecular replacement

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Processing

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

2spj


Resolution: 1.451→46.751 Å / SU ML: 0.13 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 18.54 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1812 5471 4.91 %
Rwork0.1632 105945 -
obs0.1641 111416 99.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 72.98 Å2 / Biso mean: 22.9199 Å2 / Biso min: 10.4 Å2
Refinement stepCycle: final / Resolution: 1.451→46.751 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4934 0 49 463 5446
Biso mean--34.51 30.11 -
Num. residues----602
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0055207
X-RAY DIFFRACTIONf_angle_d0.7867053
X-RAY DIFFRACTIONf_chiral_restr0.08727
X-RAY DIFFRACTIONf_plane_restr0.005927
X-RAY DIFFRACTIONf_dihedral_angle_d5.2773175
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork
1.451-1.46750.27761780.25983470
1.4675-1.48480.26591730.24043576
1.4848-1.50290.26821840.22073525
1.5029-1.52190.2181740.2143495
1.5219-1.54190.21392070.20943587
1.5419-1.5630.20981770.20563445
1.563-1.58540.241820.19853594
1.5854-1.6090.23991810.19153444
1.609-1.63420.20361630.18663606
1.6342-1.6610.1931800.17893463
1.661-1.68960.19451950.17263576
1.6896-1.72030.17681870.16963449
1.7203-1.75340.17692130.16923547
1.7534-1.78920.19451740.16743527
1.7892-1.82810.21331800.16893518
1.8281-1.87070.21081860.16353540
1.8707-1.91740.17661780.16623537
1.9174-1.96930.18032070.1613516
1.9693-2.02720.18841800.15733530
2.0272-2.09270.19941900.15853507
2.0927-2.16750.18831750.16083528
2.1675-2.25420.15711720.15713567
2.2542-2.35680.18431860.15833540
2.3568-2.48110.18841680.16173543
2.4811-2.63650.19851510.16773560
2.6365-2.84010.17941650.15993550
2.8401-3.12580.18311890.16143541
3.1258-3.5780.15621970.14993535
3.578-4.50730.15411920.14093550
4.5073-100.16841870.1623579

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