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- PDB-7ome: Azacoelenterazine-bound Renilla-type engineered ancestral lucifer... -

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Basic information

Entry
Database: PDB / ID: 7ome
TitleAzacoelenterazine-bound Renilla-type engineered ancestral luciferase variant (AncFT7)
ComponentsRenilla-type engineered ancestral luciferase variant (AncFT7)
KeywordsLUMINESCENT PROTEIN / bioluminscence / azacoelenterazine-bound enzyme
Function / homologyAlpha/Beta hydrolase fold, catalytic domain / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta / Chem-VK8
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.501 Å
AuthorsSchenkmayerova, A. / Janin, Y.L. / Marek, M.
Funding support Czech Republic, 1items
OrganizationGrant numberCountry
European CommissionMSCA-IF-2017 792772 Czech Republic
CitationJournal: To Be Published
Title: Structural and chemical basis of the Renilla-type bioluminescence
Authors: Schenkmayerova, A. / Janin, Y. / Damborsky, J. / Marek, M.
History
DepositionMay 21, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 1, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 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: Renilla-type engineered ancestral luciferase variant (AncFT7)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,3952
Polymers35,9711
Non-polymers4241
Water3,801211
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area11800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.076, 64.487, 98.096
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Renilla-type engineered ancestral luciferase variant (AncFT7)


Mass: 35970.699 Da / Num. of mol.: 1
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-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.: 1 / Source method: obtained synthetically / Formula: C25H20N4O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 211 / 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: 1.89 Å3/Da / Density % sol: 35.05 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 9 / Details: PEG1500, SPG buffer

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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: Jul 12, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.5→43.08 Å / Num. obs: 44303 / % possible obs: 99.4 % / Redundancy: 11.5 % / CC1/2: 0.998 / Rmerge(I) obs: 0.211 / Rpim(I) all: 0.063 / Rrim(I) all: 0.221 / Net I/σ(I): 12.7 / Num. measured all: 508534 / Scaling rejects: 235
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
1.5-1.535.41.4951081619930.440.6911.6591.492.1
8.22-43.0810.20.032342533610.010.03445.399.6

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
XDSdata reduction
Aimless0.7.3data scaling
PHASERphasing
PHENIX1.14_3260refinement
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2PSJ

2psj


Resolution: 1.501→39.441 Å / SU ML: 0.13 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 18.31 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1902 2130 4.82 %
Rwork0.1682 42068 -
obs0.1693 44198 99.34 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 77.4 Å2 / Biso mean: 18.6716 Å2 / Biso min: 5.62 Å2
Refinement stepCycle: final / Resolution: 1.501→39.441 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2396 0 32 211 2639
Biso mean--20.67 28.53 -
Num. residues----295
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.501-1.53590.28291400.2709258192
1.5359-1.57430.25891220.2323271698
1.5743-1.61690.20311350.20012790100
1.6169-1.66450.22031180.1842806100
1.6645-1.71820.18711370.17682800100
1.7182-1.77960.19761500.17032783100
1.7796-1.85090.19591370.17222789100
1.8509-1.93510.17921500.16322782100
1.9351-2.03710.16881510.16082808100
2.0371-2.16470.17711410.15692812100
2.1647-2.33190.19921420.14692821100
2.3319-2.56650.17851500.16462835100
2.5665-2.93780.2021370.17512850100
2.9378-3.70080.18281510.15812887100
3.7008-39.4410.17961690.15823008100
Refinement TLS params.Method: refined / Origin x: -10.121 Å / Origin y: 1.04 Å / Origin z: -13.35 Å
111213212223313233
T0.0642 Å20 Å2-0.0004 Å2-0.0665 Å20.0003 Å2--0.0743 Å2
L0.9514 °20.1559 °2-0.1787 °2-1.0875 °2-0.4426 °2--0.8281 °2
S-0.0051 Å °-0.0541 Å °0.0091 Å °-0.0408 Å °-0.0168 Å °-0.0111 Å °0.0647 Å °0.0128 Å °0.0059 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND ( RESID 12:306 OR RESID 401:401 OR RESID 501:711 ) )A12 - 306
2X-RAY DIFFRACTION1( CHAIN A AND ( RESID 12:306 OR RESID 401:401 OR RESID 501:711 ) )A401
3X-RAY DIFFRACTION1( CHAIN A AND ( RESID 12:306 OR RESID 401:401 OR RESID 501:711 ) )A501 - 711

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