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- PDB-8bo9: NanoLuc-D9R/H57A/K89R mutant complexed with azacoelenterazine bou... -

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Basic information

Entry
Database: PDB / ID: 8bo9
TitleNanoLuc-D9R/H57A/K89R mutant complexed with azacoelenterazine bound in intra-barrel catalytic site
ComponentsNon structural polyprotein
KeywordsLUMINESCENT PROTEIN / Nanoluc-type luciferase with bound substrate analogue - azacoelenterazine
Function / homologyCalycin / Chem-NSW / Non structural polyprotein
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.1 Å
AuthorsMarek, M. / Janin, L.Y.
Funding support Czech Republic, 1items
OrganizationGrant numberCountry
Czech Science FoundationGA22-09853S Czech Republic
CitationJournal: Nat Commun / Year: 2023
Title: Illuminating the mechanism and allosteric behavior of NanoLuc luciferase.
Authors: Nemergut, M. / Pluskal, D. / Horackova, J. / Sustrova, T. / Tulis, J. / Barta, T. / Baatallah, R. / Gagnot, G. / Novakova, V. / Majerova, M. / Sedlackova, K. / Marques, S.M. / Toul, M. / ...Authors: Nemergut, M. / Pluskal, D. / Horackova, J. / Sustrova, T. / Tulis, J. / Barta, T. / Baatallah, R. / Gagnot, G. / Novakova, V. / Majerova, M. / Sedlackova, K. / Marques, S.M. / Toul, M. / Damborsky, J. / Prokop, Z. / Bednar, D. / Janin, Y.L. / Marek, M.
History
DepositionNov 15, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 27, 2023Provider: repository / Type: Initial release
Revision 1.1Dec 13, 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.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Non structural polyprotein
B: Non structural polyprotein
C: Non structural polyprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,4536
Polymers61,1773
Non-polymers1,2763
Water36020
1
A: Non structural polyprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,8182
Polymers20,3921
Non-polymers4251
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Non structural polyprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,8182
Polymers20,3921
Non-polymers4251
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Non structural polyprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,8182
Polymers20,3921
Non-polymers4251
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)147.907, 112.601, 59.703
Angle α, β, γ (deg.)90.000, 90.800, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Non structural polyprotein


Mass: 20392.291 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli) / References: UniProt: A0A482LYE4
#2: Chemical ChemComp-NSW / 3-(4-hydroxyphenyl)-8-[(4-hydroxyphenyl)methyl]-5-(phenylmethyl)-1$l^{4},4,7,8-tetrazabicyclo[4.3.0]nona-1(6),2,4-trien-9-one


Mass: 425.459 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C25H21N4O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 20 / 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: 3 Å3/Da / Density % sol: 69.73 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 5.5 / Details: PEG 10000, ammonium acetate, Bis-tris

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 7, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.1→49.49 Å / Num. obs: 17550 / % possible obs: 98.5 % / Redundancy: 3.5 % / CC1/2: 0.997 / Net I/σ(I): 6
Reflection shellResolution: 3.1→3.31 Å / Num. unique obs: 3209 / CC1/2: 0.219

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
XDSdata reduction
Aimlessdata scaling
PHASERphasing
PHENIX1.14-3260-0000refinement
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7VSX

7vsx


Resolution: 3.1→46.771 Å / SU ML: 0.6 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 43.01 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3074 894 5.18 %
Rwork0.2724 16381 -
obs0.2742 17275 96.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 197.33 Å2 / Biso mean: 109.6414 Å2 / Biso min: 50.88 Å2
Refinement stepCycle: final / Resolution: 3.1→46.771 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4090 0 96 20 4206
Biso mean--104.32 98.5 -
Num. residues----519
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
3.1-3.29420.46771360.4509256391
3.2942-3.54850.43081590.3759275098
3.5485-3.90540.35921570.3272270597
3.9054-4.47010.29841470.2786279599
4.4701-5.63040.2751530.2683276798
5.6304-46.7710.2731420.2219280197

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