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- PDB-24nk: Crystal Structure of Cypridina Luciferase complexed with Oxyluciferin -

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Basic information

Entry
Database: PDB / ID: 24nk
TitleCrystal Structure of Cypridina Luciferase complexed with Oxyluciferin
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 / MOLECULAR REPLACEMENT / Resolution: 3.14 Å
AuthorsKihira, K. / Wu, C. / Kanie, S. / 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)60,5984
Polymers59,7621
Non-polymers8363
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)144.648, 144.648, 186.154
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
Details: Signal peptides (residues 1-18, MKTLILAVALVYCATVHC) are trimmed during CLuc maturation.
Source: (gene. exp.) Cypridina noctiluca (crustacean) / Gene: CnL / 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
#3: Chemical ChemComp-A1L7I / (2~{S})-~{N}-[3-[3-[bis(azanyl)methylideneamino]propyl]-5-(1~{H}-indol-3-yl)pyrazin-2-yl]-2-methyl-butanamide


Mass: 393.485 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H27N7O / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
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: 4.61 Å3/Da / Density % sol: 73.31 %
Crystal growTemperature: 293 K / Method: counter-diffusion / pH: 7
Details: 25mg/mL CLuc complexed with oxyluciferin, 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-17A / Wavelength: 0.98 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 5, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 3.14→47.35 Å / Num. obs: 20708 / % possible obs: 99.8 % / Redundancy: 19.5 % / CC1/2: 0.999 / Rmerge(I) obs: 0.221 / Rpim(I) all: 0.071 / Rrim(I) all: 0.233 / Χ2: 1.07 / Net I/σ(I): 14
Reflection shellResolution: 3.14→3.36 Å / Redundancy: 20.5 % / Rmerge(I) obs: 1.679 / Mean I/σ(I) obs: 2.6 / Num. unique obs: 3653 / CC1/2: 0.981 / Rpim(I) all: 0.533 / Rrim(I) all: 1.762 / Χ2: 0.99 / % possible all: 99.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
XDSdata reduction
Aimlessdata scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.14→47.35 Å / Cor.coef. Fo:Fc: 0.905 / Cor.coef. Fo:Fc free: 0.883 / SU B: 70.502 / SU ML: 0.472 / Cross valid method: THROUGHOUT / ESU R: 0.94 / ESU R Free: 0.473 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.32481 1043 5 %RANDOM
Rwork0.26561 ---
obs0.2685 19624 99.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 124.53 Å2
Baniso -1Baniso -2Baniso -3
1-7.56 Å23.78 Å20 Å2
2--7.56 Å2-0 Å2
3----24.52 Å2
Refinement stepCycle: 1 / Resolution: 3.14→47.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4017 0 57 0 4074
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0124181
X-RAY DIFFRACTIONr_bond_other_d0.0010.0163822
X-RAY DIFFRACTIONr_angle_refined_deg1.8891.8365684
X-RAY DIFFRACTIONr_angle_other_deg0.5921.7738861
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9625514
X-RAY DIFFRACTIONr_dihedral_angle_2_deg5.347522
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.32910690
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0780.2621
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.024897
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02921
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_it12.8117.8932062
X-RAY DIFFRACTIONr_mcbond_other12.8117.8932062
X-RAY DIFFRACTIONr_mcangle_it18.71714.1912574
X-RAY DIFFRACTIONr_mcangle_other18.71414.192575
X-RAY DIFFRACTIONr_scbond_it14.4928.6562119
X-RAY DIFFRACTIONr_scbond_other14.4918.6572120
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other20.68215.653111
X-RAY DIFFRACTIONr_long_range_B_refined25.49297.5417450
X-RAY DIFFRACTIONr_long_range_B_other25.49297.5417451
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.14→3.221 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.469 77 -
Rwork0.473 1407 -
obs--99.26 %
Refinement TLS params.Method: refined / Origin x: 76.5421 Å / Origin y: 4.8876 Å / Origin z: 25.2735 Å
111213212223313233
T0.5299 Å20.0234 Å2-0.0031 Å2-0.0953 Å20.0303 Å2--0.5349 Å2
L0.6846 °20.4409 °20.3484 °2-1.4587 °20.94 °2--2.1554 °2
S-0.004 Å °0.0789 Å °-0.0394 Å °-0.2799 Å °-0.0368 Å °-0.0408 Å °0.0071 Å °0.3324 Å °0.0409 Å °

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