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- PDB-7sny: 2.10A Resolution Structure of NanoBiT Complementation Reporter La... -

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Basic information

Entry
Database: PDB / ID: 7sny
Title2.10A Resolution Structure of NanoBiT Complementation Reporter Large Subunit LgBiT
ComponentsOplophorus-luciferin 2-monooxygenase catalytic subunit
KeywordsOXIDOREDUCTASE / OPLOPHORUS BIOLUMINESCENT PROTEIN / NANOLUC LUCIFERASE / NLUC / COELENTERAZINE / FURIMAZINE / BETA-BARREL / Split reporter
Function / homology
Function and homology information


Oplophorus-luciferin 2-monooxygenase / Oplophorus-luciferin 2-monooxygenase activity / bioluminescence / extracellular region
Similarity search - Function
Calycin beta-barrel core domain / Calycin / Lipocalin / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Oplophorus-luciferin 2-monooxygenase catalytic subunit
Similarity search - Component
Biological speciesOplophorus gracilirostris (crustacean)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.1 Å
AuthorsLovell, S. / Mehzabeen, N. / Battaile, K.P. / Wood, M.G. / Encell, L.P. / Wood, K.V.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)P30 GM110761 United States
CitationJournal: To be published
Title: 2.10A Resolution Structure of NanoBiT Complementation Reporter Large Subunit LgBiT
Authors: Encell, L.P. / Lovell, S. / Mehzabeen, N. / Battaile, K.P. / Wood, M.G. / Wood, K.V.
History
DepositionOct 28, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 16, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: 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: Oplophorus-luciferin 2-monooxygenase catalytic subunit


Theoretical massNumber of molelcules
Total (without water)18,5721
Polymers18,5721
Non-polymers00
Water57632
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)62.342, 62.342, 104.811
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein Oplophorus-luciferin 2-monooxygenase catalytic subunit / 19kOLase


Mass: 18572.107 Da / Num. of mol.: 1 / Fragment: M-1 to S157
Mutation: A4E, Q11E, G15A, Q18L, L27V, F31L, A33N, G35A, K43R, V44I, L46R, G51A, A54I, G67A, F68D, G71A, L72Q, M75E, I76V, I90V, H93P, I107L, D108N, P115E, Q124K, Y138I, N144T, L149M, G157S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oplophorus gracilirostris (crustacean) / Plasmid: pFN18K(+AIA) / Production host: Escherichia coli KRX (bacteria)
References: UniProt: Q9GV45, Oplophorus-luciferin 2-monooxygenase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 32 / Source method: isolated from a natural source / Formula: H2O

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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: 2.74 Å3/Da / Density % sol: 55.14 % / Mosaicity: 0.08 °
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 5
Details: 15% (v/v) 2-methyl-2,4-pentanediol, 0.1 M sodium acetate, 2% (w/v) PEG 4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 28, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.1→40.63 Å / Num. obs: 12596 / % possible obs: 99.7 % / Redundancy: 12.9 % / Biso Wilson estimate: 44.54 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.083 / Rpim(I) all: 0.024 / Rrim(I) all: 0.087 / Net I/σ(I): 17.6 / Num. measured all: 162972 / Scaling rejects: 12
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
2.1-2.1613.61.793135369980.7570.4991.8621.999.5
8.91-40.63110.03623162110.9990.0120.03859.899.3

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.1 Å40.64 Å
Translation2.1 Å40.64 Å

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Processing

Software
NameVersionClassification
XDSdata reduction
Aimless0.5.1data scaling
PHASER2.5.7phasing
PHENIXdev_4289refinement
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5IBO

5ibo


Resolution: 2.1→33.73 Å / SU ML: 0.27 / Cross valid method: THROUGHOUT / σ(F): 1.11 / Phase error: 29.73 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2769 614 4.89 %
Rwork0.2208 11955 -
obs0.2234 12569 99.38 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 143.7 Å2 / Biso mean: 55.3402 Å2 / Biso min: 26.3 Å2
Refinement stepCycle: final / Resolution: 2.1→33.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1220 0 0 32 1252
Biso mean---47.06 -
Num. residues----159
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 4

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.1-2.310.2871490.2492893304299
2.31-2.650.30261580.26732924308299
2.65-3.330.28551610.256329583119100
3.33-33.730.26551460.196331803326100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.47481.43631.47360.9443-0.04661.4613-0.16770.5584-0.4665-0.32670.1172-0.08-0.0047-0.1543-0.00240.40620.0250.0920.3080.02820.33224.3822-2.05167.2104
20.45540.6068-0.17631.0691-0.03180.3516-0.28030.13660.2414-0.10910.2288-0.1427-0.25640.1937-0.00010.4409-0.05050.10910.4505-0.01990.45214.17296.824467.7683
30.19930.81610.1065-0.7456-0.80071.19810.22260.0007-0.0705-0.2892-0.010.09590.145-0.17790.00040.42560.13110.0250.4323-0.00930.4207-9.3708-1.361558.7039
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 0 through 61 )A0 - 61
2X-RAY DIFFRACTION2chain 'A' and (resid 62 through 98 )A62 - 98
3X-RAY DIFFRACTION3chain 'A' and (resid 99 through 163 )A99 - 163

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