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- PDB-24ne: Crystal Structure of Cypridina luciferase -

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Basic information

Entry
Database: PDB / ID: 24ne
TitleCrystal Structure of Cypridina luciferase
ComponentsLuciferase
KeywordsLUMINESCENT PROTEIN / luciferase
Function / homology: / von Willebrand factor, type D domain / von Willebrand factor type D domain / VWFD domain profile. / von Willebrand factor (vWF) type D domain / extracellular matrix / : / Luciferase
Function and homology information
Biological speciesCypridina noctiluca (crustacean)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3 Å
AuthorsKihira, K. / Yasuno, R. / Mitani, Y. / Ohmiya, Y.
Funding support Japan, 1items
OrganizationGrant numberCountry
Ministry of Education, Culture, Sports, Science and Technology (Japan)22H02692 Japan
CitationJournal: Int.J.Biol.Macromol. / Year: 2026
Title: Three-dimensional structure of Cypridina luciferase illuminates the mechanism of bioluminescence of imidazopyrazinone-type luciferin.
Authors: Kihira, K. / Yasuno, R. / Kanie, S. / Wu, C. / Mitani, Y. / Ohmiya, Y.
History
DepositionMar 12, 2026Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 8, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Luciferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,2053
Polymers59,7621
Non-polymers4422
Water00
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)144.370, 144.370, 186.710
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number182
Space group name H-MP6322

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Components

#1: Protein Luciferase


Mass: 59762.234 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Cypridina noctiluca (crustacean) / Gene: CnL / Plasmid: pcDNA3.4-TOPO / Cell line (production host): Expi293F GnTI- / Production host: Homo sapiens (human) / References: UniProt: Q75R40
#2: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
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: 4.56 Å3/Da / Density % sol: 73.05 %
Crystal growTemperature: 293 K / Method: counter-diffusion / pH: 7
Details: 25mg/mL CLuc, 3% polyethylene glycol monomethyl ether 2000, 7% polypropylene glycol 400, 2M ammonium phosphate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-1A / Wavelength: 2.70001 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Feb 18, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 2.70001 Å / Relative weight: 1
ReflectionResolution: 2.8→47.3 Å / Num. obs: 53534 / % possible obs: 99.7 % / Redundancy: 294 % / Biso Wilson estimate: 59.67 Å2 / CC1/2: 1 / Rrim(I) all: 0.205 / Net I/σ(I): 48.94
Reflection shellResolution: 2.8→2.97 Å / Redundancy: 152 % / Mean I/σ(I) obs: 2.73 / Num. unique obs: 8599 / CC1/2: 0.983 / Rrim(I) all: 2.878 / % possible all: 98.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
XSCALEdata scaling
XDSdata reduction
CRANK2phasing
RefinementMethod to determine structure: SAD / Resolution: 3→47.3 Å / Cor.coef. Fo:Fc: 0.928 / Cor.coef. Fo:Fc free: 0.914 / SU B: 35.033 / SU ML: 0.281 / Cross valid method: THROUGHOUT / ESU R: 0.571 / ESU R Free: 0.348
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.26841 1198 5.1 %RANDOM
Rwork0.23307 ---
obs0.23488 22456 99.91 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 100.966 Å2
Baniso -1Baniso -2Baniso -3
1-5.61 Å22.8 Å20 Å2
2--5.61 Å2-0 Å2
3----18.19 Å2
Refinement stepCycle: 1 / Resolution: 3→47.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4017 0 28 0 4045
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0124150
X-RAY DIFFRACTIONr_bond_other_d0.0010.0163794
X-RAY DIFFRACTIONr_angle_refined_deg1.4621.8275642
X-RAY DIFFRACTIONr_angle_other_deg0.4671.7658802
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6835514
X-RAY DIFFRACTIONr_dihedral_angle_2_deg3.516522
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.31510690
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0670.2620
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.024868
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02908
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it8.3836.7622062
X-RAY DIFFRACTIONr_mcbond_other8.3796.7612062
X-RAY DIFFRACTIONr_mcangle_it11.88812.1912574
X-RAY DIFFRACTIONr_mcangle_other11.88512.1912575
X-RAY DIFFRACTIONr_scbond_it8.9917.2472088
X-RAY DIFFRACTIONr_scbond_other8.9897.2492089
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other12.73713.1773069
X-RAY DIFFRACTIONr_long_range_B_refined17.43882.3816888
X-RAY DIFFRACTIONr_long_range_B_other17.43982.3816889
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3→3.078 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.484 78 -
Rwork0.324 1626 -
obs--99.94 %
Refinement TLS params.Method: refined / Origin x: 76.4256 Å / Origin y: 4.7421 Å / Origin z: 25.3396 Å
111213212223313233
T0.3768 Å20.0492 Å20.0302 Å2-0.0299 Å20.0158 Å2--0.2867 Å2
L0.7576 °20.9322 °20.7506 °2-1.9853 °21.2698 °2--2.5468 °2
S-0.028 Å °0.0699 Å °-0.0682 Å °-0.2666 Å °0.0559 Å °-0.1284 Å °0.0619 Å °0.2387 Å °-0.0279 Å °

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