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- PDB-2d1q: Crystal structure of the thermostable Japanese Firefly Luciferase... -

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Basic information

Entry
Database: PDB / ID: 2d1q
TitleCrystal structure of the thermostable Japanese Firefly Luciferase complexed with MgATP
ComponentsLuciferin 4-monooxygenase
KeywordsOXIDOREDUCTASE / ALPHA/BETA / BETA BARREL / ALPHA+BETA / RIKEN Structural Genomics/Proteomics Initiative / RSGI / Structural Genomics
Function / homology
Function and homology information


Photinus-luciferin 4-monooxygenase (ATP-hydrolyzing) activity / firefly luciferase / CoA-ligase activity / bioluminescence / peroxisome / ATP binding / metal ion binding
Similarity search - Function
Rossmann fold - #980 / Luciferase; domain 3 / Luciferase; Domain 3 / ANL, C-terminal domain / AMP-binding enzyme C-terminal domain / AMP-binding enzyme, C-terminal domain / AMP-binding, conserved site / Putative AMP-binding domain signature. / AMP-dependent synthetase/ligase / AMP-binding enzyme ...Rossmann fold - #980 / Luciferase; domain 3 / Luciferase; Domain 3 / ANL, C-terminal domain / AMP-binding enzyme C-terminal domain / AMP-binding enzyme, C-terminal domain / AMP-binding, conserved site / Putative AMP-binding domain signature. / AMP-dependent synthetase/ligase / AMP-binding enzyme / GMP Synthetase; Chain A, domain 3 / AMP-binding enzyme, C-terminal domain superfamily / Roll / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
ADENOSINE MONOPHOSPHATE / Luciferin 4-monooxygenase
Similarity search - Component
Biological speciesLuciola cruciata (Japanese firefly)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsNakatsu, T. / Ichiyama, S. / Hiratake, J. / Saldanha, A. / Kobashi, N. / Sakata, K. / Kato, H. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: Nature / Year: 2006
Title: Structural basis for the spectral difference in luciferase bioluminescence.
Authors: Nakatsu, T. / Ichiyama, S. / Hiratake, J. / Saldanha, A. / Kobashi, N. / Sakata, K. / Kato, H.
History
DepositionAug 31, 2005Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 21, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 31, 2018Group: Experimental preparation / Category: exptl_crystal_grow
Item: _exptl_crystal_grow.pdbx_details / _exptl_crystal_grow.temp
Revision 1.4Nov 10, 2021Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.6Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.7Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Luciferin 4-monooxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,4802
Polymers60,1331
Non-polymers3471
Water3,297183
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)57.780, 181.975, 53.566
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Luciferin 4-monooxygenase / Luciferase


Mass: 60133.156 Da / Num. of mol.: 1 / Mutation: T217I
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Luciola cruciata (Japanese firefly) / Plasmid: PUC18 / Production host: Escherichia coli (E. coli) / Strain (production host): HB101 / References: UniProt: P13129, firefly luciferase
#2: Chemical ChemComp-AMP / ADENOSINE MONOPHOSPHATE


Mass: 347.221 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H14N5O7P / Comment: AMP*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 183 / Source method: isolated from a natural source / Formula: H2O
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: 2.35 Å3/Da / Density % sol: 47.2 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 8.5
Details: PEG4000, Lithium chrolide, ATP, magnesium chloride, Tris-HCl, pH 8.5, VAPOR DIFFUSION, temperature 293K

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Dec 16, 1999
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.3→60 Å / Num. all: 25394 / Num. obs: 25394 / % possible obs: 97.9 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 3.1 % / Rmerge(I) obs: 0.058 / Net I/σ(I): 10.7
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 2.55 % / Rmerge(I) obs: 0.15 / Mean I/σ(I) obs: 4 / Num. unique all: 2304 / % possible all: 91.1

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
CrystalClear(MSC/RIGAKU)data reduction
CrystalClear(MSC/RIGAKU)data scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1LCI

1lci


Resolution: 2.3→60 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.91 / SU B: 6.834 / SU ML: 0.165 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.319 / ESU R Free: 0.224 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.22766 1291 5.1 %RANDOM
Rwork0.17898 ---
all0.18151 25353 --
obs0.18151 24062 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 22.972 Å2
Baniso -1Baniso -2Baniso -3
1--1.64 Å20 Å20 Å2
2---0.18 Å20 Å2
3---1.81 Å2
Refinement stepCycle: LAST / Resolution: 2.3→60 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3976 0 23 183 4182
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0224081
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2641.985556
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7035529
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0820.2657
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.023026
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1930.21616
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1340.2179
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1940.220
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1410.28
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.6141.52632
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.15124250
X-RAY DIFFRACTIONr_scbond_it1.71431449
X-RAY DIFFRACTIONr_scangle_it2.9324.51306
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.251 92
Rwork0.218 1588

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