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- PDB-7snx: 1.70A Resolution Structure of NanoBiT Complementation Reporter Co... -

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Basic information

Entry
Database: PDB / ID: 7snx
Title1.70A Resolution Structure of NanoBiT Complementation Reporter Complex of LgBit and SmBiT Subunits
Components
  • Oplophorus-luciferin 2-monooxygenase catalytic subunit
  • Oplophorus-luciferin 2-monooxygenase catalytic subunit: C-terminal Peptide (11-mer)
KeywordsOXIDOREDUCTASE / OPLOPHORUS BIOLUMINESCENT PROTEIN / NANOLUC LUCIFERASE / NLUC / COELENTERAZINE / FURIMAZINE / BETA-BARREL / Split reporter / split luciferase / HiBiT / ternary Nluc / LgTrip
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: 1.7 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: 1.70A Resolution Structure of NanoBiT Complementation Reporter Complex of LgBit and SmBiT Subunits
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
Revision 1.2Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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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
B: Oplophorus-luciferin 2-monooxygenase catalytic subunit: C-terminal Peptide (11-mer)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,5893
Polymers19,4972
Non-polymers921
Water3,495194
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2230 Å2
ΔGint-10 kcal/mol
Surface area8410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.418, 73.418, 101.109
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212

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Components

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


Mass: 18130.572 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: Protein/peptide Oplophorus-luciferin 2-monooxygenase catalytic subunit: C-terminal Peptide (11-mer) / 19kOLase


Mass: 1366.582 Da / Num. of mol.: 1 / Mutation: W161Y, C164F, N166E / Source method: obtained synthetically / Source: (synth.) Oplophorus gracilirostris (crustacean) / References: UniProt: Q9GV45
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 194 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationY

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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: 3.49 Å3/Da / Density % sol: 64.8 % / Mosaicity: 0.08 °
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 5.6 / Details: 1.5 M Na/K Phosphate, 4 (v/v) % 1,3-propanediol

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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: Apr 26, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.7→46.18 Å / Num. obs: 31166 / % possible obs: 100 % / Redundancy: 6.9 % / Biso Wilson estimate: 16.67 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.116 / Net I/σ(I): 12.2 / Num. measured all: 214426 / Scaling rejects: 5
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Net I/σ(I) obs% possible all
1.7-1.737.11.3071152716270.5351.6100
9-46.185.80.03315902730.99937.399.5

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation1.75 Å36.71 Å
Translation1.75 Å36.71 Å

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Processing

Software
NameVersionClassification
XDSdata reduction
Aimless0.7.7data scaling
PHASER2.5.7phasing
PHENIXdev_4289refinement
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5IBO

5ibo


Resolution: 1.7→36.71 Å / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 1.09 / Phase error: 16.59 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1785 1622 5.22 %
Rwork0.1567 29480 -
obs0.1578 31102 99.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 61.25 Å2 / Biso mean: 20.6458 Å2 / Biso min: 9.72 Å2
Refinement stepCycle: final / Resolution: 1.7→36.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1316 0 6 194 1516
Biso mean--41.98 32.16 -
Num. residues----168
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 12 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.7-1.750.2931270.244524222549
1.75-1.810.27381360.223323952531
1.81-1.870.20861240.192124302554
1.87-1.950.18941280.17424152543
1.95-2.030.18061070.147524442551
2.03-2.140.18121470.140824112558
2.14-2.280.15621560.136124112567
2.28-2.450.16771310.138924622593
2.45-2.70.15851270.147524492576
2.7-3.090.19711400.144924792619
3.09-3.890.14921530.14425042657
3.89-36.710.17741460.16526582804
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)
11.27730.28320.11291.27770.51671.65060.0048-0.017-0.0772-0.0170.0133-0.02430.07640.005-0.01540.11920.00530.01650.13140.0030.121164.355940.681331.9015
21.02130.7892-0.0891.7284-0.34180.56350.1395-0.1313-0.01840.1999-0.10130.17650.0968-0.0839-0.03150.1729-0.0216-0.0070.1438-0.00090.162956.300335.075941.3524
30.62540.1660.47120.21010.23851.47330.00170.04320.0264-0.0582-0.0266-0.0235-0.0490.08590.0250.1380.0023-0.00770.12180.00430.133572.560945.396432.8923
42.3876-0.56530.31461.4477-0.08041.68350.03040.04910.01920.1349-0.00050.0070.0259-0.0102-0.02150.14420.00540.00390.09610.00450.119764.409939.260926.2877
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 0 through 50 )A0 - 50
2X-RAY DIFFRACTION2chain 'A' and (resid 51 through 98 )A51 - 98
3X-RAY DIFFRACTION3chain 'A' and (resid 99 through 156 )A99 - 156
4X-RAY DIFFRACTION4chain 'B' and (resid 158 through 167 )B158 - 167

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