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- PDB-5b0u: Crystal structure of the mutated 19 kDa protein of Oplophorus luc... -

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Basic information

Entry
Database: PDB / ID: 5b0u
TitleCrystal structure of the mutated 19 kDa protein of Oplophorus luciferase (nanoKAZ)
ComponentsOplophorus-luciferin 2-monooxygenase catalytic subunit
KeywordsLUMINESCENT PROTEIN / Oplophorus luciferase
Function / homologyOplophorus-luciferin 2-monooxygenase / Oplophorus-luciferin 2-monooxygenase activity / Calycin / bioluminescence / extracellular region / Oplophorus-luciferin 2-monooxygenase catalytic subunit
Function and homology information
Biological speciesOplophorus gracilirostris (crustacean)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.71 Å
AuthorsTomabechi, Y. / Ehara, H. / Sekine, S.I. / Shirouzu, M.
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2016
Title: Crystal structure of nanoKAZ: The mutated 19 kDa component of Oplophorus luciferase catalyzing the bioluminescent reaction with coelenterazine
Authors: Tomabechi, Y. / Hosoya, T. / Ehara, H. / Sekine, S. / Shirouzu, M. / Inouye, S.
History
DepositionNov 4, 2015Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 13, 2016Provider: repository / Type: Initial release
Revision 1.1Jan 27, 2016Group: Database references
Revision 1.2Feb 10, 2016Group: Database references
Revision 1.3Feb 26, 2020Group: Data collection / Database references / Derived calculations
Category: citation / diffrn_source / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_oper_list.symmetry_operation
Revision 1.4Mar 20, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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


Theoretical massNumber of molelcules
Total (without water)43,0352
Polymers43,0352
Non-polymers00
Water5,981332
1
A: Oplophorus-luciferin 2-monooxygenase catalytic subunit


Theoretical massNumber of molelcules
Total (without water)21,5181
Polymers21,5181
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Oplophorus-luciferin 2-monooxygenase catalytic subunit


Theoretical massNumber of molelcules
Total (without water)21,5181
Polymers21,5181
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)79.067, 79.067, 123.425
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number94
Space group name H-MP42212
Components on special symmetry positions
IDModelComponents
11B-361-

HOH

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Components

#1: Protein Oplophorus-luciferin 2-monooxygenase catalytic subunit / 19 kDa protein of Oplophorus luciferase / nanoKAZ


Mass: 21517.520 Da / Num. of mol.: 2
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) / Production host: Escherichia coli (E. coli) / References: UniProt: Q9GV45
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 332 / 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: 2.24 Å3/Da / Density % sol: 45.12 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 1.1 M di-ammonium tartrate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 27, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.71→50 Å / Num. obs: 47630 / % possible obs: 99.9 % / Redundancy: 14.2 % / Net I/σ(I): 33.17
Reflection shellResolution: 1.71→1.74 Å / Redundancy: 12.4 % / Rmerge(I) obs: 0.948 / Mean I/σ(I) obs: 2.8 / % possible all: 99.9

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASER2.5.5phasing
PHENIX1.9_1690refinement
PDB_EXTRACT3.15data extraction
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 1.71→48.648 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.09 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2264 1805 4.2 %
Rwork0.2013 41202 -
obs0.2024 43007 99.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 90.32 Å2 / Biso mean: 30.6785 Å2 / Biso min: 13.16 Å2
Refinement stepCycle: final / Resolution: 1.71→48.648 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2688 0 0 332 3020
Biso mean---37.14 -
Num. residues----339
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0092748
X-RAY DIFFRACTIONf_angle_d1.2253731
X-RAY DIFFRACTIONf_chiral_restr0.051420
X-RAY DIFFRACTIONf_plane_restr0.005479
X-RAY DIFFRACTIONf_dihedral_angle_d12.267989
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.71-1.75630.28071360.25613110X-RAY DIFFRACTION100
1.7563-1.80790.2761370.24053137X-RAY DIFFRACTION100
1.8079-1.86630.24391350.2263088X-RAY DIFFRACTION100
1.8663-1.9330.25661380.22113138X-RAY DIFFRACTION100
1.933-2.01040.23051360.21613122X-RAY DIFFRACTION100
2.0104-2.10190.23421380.20883117X-RAY DIFFRACTION100
2.1019-2.21270.22671370.20623146X-RAY DIFFRACTION100
2.2127-2.35130.23581380.20813146X-RAY DIFFRACTION100
2.3513-2.53290.21251390.20763172X-RAY DIFFRACTION100
2.5329-2.78770.24011400.20623172X-RAY DIFFRACTION100
2.7877-3.19110.25231400.20373211X-RAY DIFFRACTION100
3.1911-4.02010.22331420.1863241X-RAY DIFFRACTION100
4.0201-100.19651490.18753402X-RAY DIFFRACTION99

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