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- PDB-5ibo: 1.95A resolution structure of NanoLuc luciferase -

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Basic information

Entry
Database: PDB / ID: 5ibo
Title1.95A resolution structure of NanoLuc luciferase
ComponentsOplophorus-luciferin 2-monooxygenase catalytic subunit
KeywordsOXIDOREDUCTASE / Oplophorus bioluminescent protein / NanoLuc luciferase / NLuc / coelenterazine / furimazine / beta-barrel
Function / homologyOplophorus-luciferin 2-monooxygenase / Oplophorus-luciferin 2-monooxygenase activity / Calycin / bioluminescence / extracellular region / DECANOIC ACID / Oplophorus-luciferin 2-monooxygenase catalytic subunit
Function and homology information
Biological speciesOplophorus gracilirostris (crustacean)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.95 Å
AuthorsLovell, S. / Mehzabeen, N. / Battaile, K.P. / Wood, M.G. / Encell, L.P. / Wood, K.V.
CitationJournal: To be published
Title: To be determined
Authors: Lovell, S. / Mehzabeen, N. / Battaile, K.P. / Wood, M.G. / Encell, L.P. / Wood, K.V.
History
DepositionFeb 22, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 13, 2016Provider: repository / Type: Initial release
Revision 1.1Mar 6, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_prerelease_seq / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Oplophorus-luciferin 2-monooxygenase catalytic subunit
B: Oplophorus-luciferin 2-monooxygenase catalytic subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,2034
Polymers38,8582
Non-polymers3452
Water1,26170
1
A: Oplophorus-luciferin 2-monooxygenase catalytic subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,6012
Polymers19,4291
Non-polymers1721
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Oplophorus-luciferin 2-monooxygenase catalytic subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,6012
Polymers19,4291
Non-polymers1721
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)60.436, 62.658, 96.835
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

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


Mass: 19429.164 Da / Num. of mol.: 2 / Fragment: Full Length
Mutation: A4E, Q11R, Q18L, L27V, A33N, K43R, V44I, A54I, F68D, L72Q, M75K, I90V, P115E, Q124K, Y138I, N166R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oplophorus gracilirostris (crustacean) / Plasmid: pFN18K(-AIA) / Production host: Escherichia coli (E. coli) / Strain (production host): KRX
References: UniProt: Q9GV45, Oplophorus-luciferin 2-monooxygenase
#2: Chemical ChemComp-DKA / DECANOIC ACID


Mass: 172.265 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H20O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 70 / 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: 2.36 Å3/Da / Density % sol: 47.86 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 20% (w/v) PEG 3350, 200 mM ammonium nitrate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 7, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.95→48.42 Å / Num. obs: 27490 / % possible obs: 99.9 % / Redundancy: 6.2 % / Biso Wilson estimate: 26.42 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.079 / Rpim(I) all: 0.034 / Rrim(I) all: 0.086 / Net I/σ(I): 17.4 / Num. measured all: 171068 / Scaling rejects: 11
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
1.95-26.10.8561100
8.94-48.425.60.02199.2

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation2.18 Å48.42 Å
Translation3.12 Å48.42 Å

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Processing

Software
NameVersionClassification
PHENIX(dev_2356: ???)refinement
Aimless0.1.29data scaling
PHASER2.5.4phasing
PDB_EXTRACT3.2data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: In-house Selenomethionine Structure

Resolution: 1.95→48.417 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 0.86 / Phase error: 24.32 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2499 1325 5.04 %
Rwork0.1883 --
obs0.1913 26285 95.56 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.95→48.417 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2576 0 24 70 2670
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0122650
X-RAY DIFFRACTIONf_angle_d1.0983596
X-RAY DIFFRACTIONf_dihedral_angle_d13.6811528
X-RAY DIFFRACTIONf_chiral_restr0.071418
X-RAY DIFFRACTIONf_plane_restr0.007458
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9501-2.02820.31441210.24172630X-RAY DIFFRACTION92
2.0282-2.12050.27471560.22922832X-RAY DIFFRACTION100
2.1205-2.23230.23181560.20262751X-RAY DIFFRACTION96
2.2323-2.37220.23271450.1992482X-RAY DIFFRACTION88
2.3722-2.55530.29841340.21152655X-RAY DIFFRACTION92
2.5553-2.81240.28651540.21262787X-RAY DIFFRACTION97
2.8124-3.21930.26411510.19772880X-RAY DIFFRACTION99
3.2193-4.05570.24641590.16892902X-RAY DIFFRACTION99
4.0557-48.43240.21551490.16493041X-RAY DIFFRACTION98
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)
10.09390.0547-0.00120.1853-0.14350.116-0.06570.1670.09340.08520.0614-0.0917-0.0783-0.0847-0.09310.07980.04670.02310.16920.04440.153455.535943.890312.8522
20.0079-0.0177-0.0110.16810.11130.0771-0.00890.26690.07010.03750.09410.26250.0888-0.05520.06050.1130.01130.04450.23090.05140.248645.642234.915912.7416
30.02350.1213-0.08270.6827-0.25770.1431-0.08450.11130.21910.30460.0147-0.0151-0.22710.0011-0.01880.03510.0355-0.01510.22350.04840.179657.401548.34436.8032
40.136-0.0961-0.0410.21250.23020.3492-0.03480.10990.13290.1755-0.06480.05-0.0372-0.1267-0.16750.55580.07980.0790.12170.03810.253745.882335.986135.2016
50.0063-0.0014-0.00120.0007-0.00120.0018-0.0025-0.022-0.08080.01510.00630.00150.0357-0.0007-00.43250.03470.0480.23670.06480.34551.878650.646229.6939
60.2457-0.04740.1030.0919-0.08780.09750.0442-0.04430.09830.28260.03460.07610.14170.08360.00620.57130.01740.00370.19650.02780.205257.264138.122138.1341
70.0974-0.08920.0480.144-0.05960.04460.1052-0.13290.14950.56570.05570.02490.18390.06190.07720.7850.03250.08620.0975-0.03620.270357.270145.87440.4993
80.10260.04520.07630.16440.20730.48770.0245-0.01240.16420.60890.09940.1844-0.4003-0.1060.25620.87620.12010.35090.0436-0.16770.076442.818837.345839.6278
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid -1 through 50 )
2X-RAY DIFFRACTION2chain 'A' and (resid 51 through 98 )
3X-RAY DIFFRACTION3chain 'A' and (resid 99 through 169 )
4X-RAY DIFFRACTION4chain 'B' and (resid -1 through 25 )
5X-RAY DIFFRACTION5chain 'B' and (resid 26 through 40 )
6X-RAY DIFFRACTION6chain 'B' and (resid 41 through 64 )
7X-RAY DIFFRACTION7chain 'B' and (resid 65 through 113 )
8X-RAY DIFFRACTION8chain 'B' and (resid 114 through 169 )

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