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- PDB-1lci: FIREFLY LUCIFERASE -

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Basic information

Entry
Database: PDB / ID: 1lci
TitleFIREFLY LUCIFERASE
ComponentsLUCIFERASE
KeywordsOXIDOREDUCTASE / MONOOXYGENASE / PHOTOPROTEIN / LUMINESCENCE
Function / homology
Function and homology information


Photinus-luciferin 4-monooxygenase (ATP-hydrolyzing) activity / firefly luciferase / bioluminescence / peroxisome / protein-folding chaperone binding / 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. / GMP Synthetase; Chain A, domain 3 / AMP-dependent synthetase/ligase ...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. / GMP Synthetase; Chain A, domain 3 / AMP-dependent synthetase/ligase / AMP-binding enzyme, C-terminal domain superfamily / AMP-binding enzyme / Roll / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Luciferin 4-monooxygenase
Similarity search - Component
Biological speciesPhotinus pyralis (common eastern firefly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 2 Å
AuthorsConti, E. / Franks, N.P. / Brick, P.
CitationJournal: Structure / Year: 1996
Title: Crystal structure of firefly luciferase throws light on a superfamily of adenylate-forming enzymes.
Authors: Conti, E. / Franks, N.P. / Brick, P.
History
DepositionJun 1, 1996Processing site: BNL
Revision 1.0Mar 26, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _pdbx_database_status.process_site

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: LUCIFERASE


Theoretical massNumber of molelcules
Total (without water)60,8191
Polymers60,8191
Non-polymers00
Water6,575365
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)119.530, 119.530, 94.680
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein LUCIFERASE /


Mass: 60818.953 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Photinus pyralis (common eastern firefly)
Production host: Escherichia coli (E. coli) / References: UniProt: P08659, firefly luciferase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 365 / 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: 2.8 Å3/Da / Density % sol: 56 %
Crystal growTemperature: 283 K / Method: microbatch under oil / pH: 7.8
Details: 2 MICROLITRE OF LUCIFERASE (20 MG/ML) IN 0.2M AMMONIUM SULFATE, 0.001M EDTA, 0.001M DTT, 10% GLYCEROL, 25% ETHYLENE GLYCOL, 0.025M TRIS-HCL PH7.8 + 2 MICROLITRE 0.5M LITHIUM SULFATE, 26% PEG ...Details: 2 MICROLITRE OF LUCIFERASE (20 MG/ML) IN 0.2M AMMONIUM SULFATE, 0.001M EDTA, 0.001M DTT, 10% GLYCEROL, 25% ETHYLENE GLYCOL, 0.025M TRIS-HCL PH7.8 + 2 MICROLITRE 0.5M LITHIUM SULFATE, 26% PEG 8000, 0.1M TRIS-HCL PH7.8 AT 10 DEGREES CELSIUS IN MICROBATCH UNDER OIL. CRYOPROTECTANT SOLUTION: 8% PEG 8000, 10% GLYCEROL, 12.5% ETHYLENE GLYCOL, 0.1M TRIS-HCL PH7.8, microbatch under oil, temperature 283K
Crystal grow
*PLUS
Temperature: 4 ℃ / Method: batch method / Details: or 10 degrees centigrade
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
120 mg/mlprotein11
2200 mMammonium sulfate11
31 mMEDTA11
41 mMdithiothreitol11
510 %(v/v)glycerol11
6125 %(v/v)ehthylene glycol11
725 mMTris-HCl11
8500-540 mMlithium sulphate12
926 %(w/v)PEG800012
10100 mMTris-HCl12

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7B / Wavelength: 0.86
DetectorType: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Jun 10, 1995
RadiationMonochromator: Y / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.86 Å / Relative weight: 1
ReflectionResolution: 2→10 Å / Num. obs: 45322 / % possible obs: 96.5 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.044 / Net I/σ(I): 11.7
Reflection shellResolution: 2→2.11 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.186 / Mean I/σ(I) obs: 4 / % possible all: 97.3
Reflection shell
*PLUS
% possible obs: 97.3 %

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Processing

Software
NameVersionClassification
X-PLOR3.1model building
X-PLOR3.1refinement
MOSFLMdata reduction
CCP4data scaling
X-PLOR3.1phasing
RefinementMethod to determine structure: MIR / Resolution: 2→10 Å / σ(F): 0
RfactorNum. reflection% reflection
Rfree0.265 -5 %
Rwork0.224 --
obs0.224 45041 96.5 %
Displacement parametersBiso mean: 29.9 Å2
Refinement stepCycle: LAST / Resolution: 2→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3967 0 0 365 4332
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.01
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.6
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d23.7
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.2
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it4.5
X-RAY DIFFRACTIONx_mcangle_it6
X-RAY DIFFRACTIONx_scbond_it6
X-RAY DIFFRACTIONx_scangle_it7.5
LS refinement shellResolution: 2→2.09 Å
RfactorNum. reflection% reflection
Rfree0.311 -5 %
Rwork0.288 5483 -
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2PARAM19.SOLTOPH.SOL
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg23.7
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.2
LS refinement shell
*PLUS
Rfactor obs: 0.288

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