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- PDB-1vpr: Crystal structure of a luciferase domain from the dinoflagellate ... -

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Basic information

Entry
Database: PDB / ID: 1vpr
TitleCrystal structure of a luciferase domain from the dinoflagellate Lingulodinium polyedrum
Componentsluciferase
KeywordsLUMINESCENT PROTEIN / beta barrel / fatty acid binding protein / lipocalin / luciferase / pH regulation
Function / homology
Function and homology information


dinoflagellate luciferase / luciferin monooxygenase activity / oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of one atom of oxygen (internal monooxygenases or internal mixed function oxidases) / bioluminescence / cytoplasmic vesicle
Similarity search - Function
Luminescent protein fold / Dinoflagellate luciferase / Dinoflagellate luciferase repeat / Dinoflagellate luciferase repeat / Dinoflagellate luciferase, N-terminal / Luciferase, helical bundle domain / Luciferase catalytic domain / Dinoflagellate luciferase repeat / Luciferase, helical bundle domain superfamily / Luciferase/LBP N-terminal domain ...Luminescent protein fold / Dinoflagellate luciferase / Dinoflagellate luciferase repeat / Dinoflagellate luciferase repeat / Dinoflagellate luciferase, N-terminal / Luciferase, helical bundle domain / Luciferase catalytic domain / Dinoflagellate luciferase repeat / Luciferase, helical bundle domain superfamily / Luciferase/LBP N-terminal domain / Luciferase helical bundle domain / Luciferase catalytic domain / Calycin beta-barrel core domain / Calycin / Lipocalin / Few Secondary Structures / Irregular / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Dinoflagellate luciferase
Similarity search - Component
Biological speciesLingulodinium polyedrum (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.8 Å
AuthorsSchultz, L.W. / Liu, L. / Cegielski, M. / Hastings, J.W.
Citation
Journal: Proc.Natl.Acad.Sci.USA / Year: 2005
Title: Crystal structure of a pH-regulated luciferase catalyzing the bioluminescent oxidation of an open tetrapyrrole
Authors: Schultz, L.W. / Liu, L. / Cegielski, M. / Hastings, J.W.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 2003
Title: Characterization and crystallization of active domains of a novel luciferase from a marine dinoflagellate
Authors: Liu, L. / Im, H. / Cegielski, M. / LeMagueres, P. / Schultz, L.W. / Krause, K.L. / Hastings, J.W.
History
DepositionNov 15, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 8, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 30, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ref_seq_dif
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: luciferase


Theoretical massNumber of molelcules
Total (without water)42,0261
Polymers42,0261
Non-polymers00
Water4,540252
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)58.989, 63.955, 96.986
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsThis is a single domain from the luciferase and is functional as a monomer.

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Components

#1: Protein luciferase


Mass: 42025.523 Da / Num. of mol.: 1 / Fragment: sequence database residues 866-1241
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lingulodinium polyedrum (eukaryote) / Plasmid: PQE-30 / Production host: Escherichia coli (E. coli) / Strain (production host): M15 / References: UniProt: O77206
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 252 / 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: 2.2 Å3/Da / Density % sol: 42 %
Crystal growTemperature: 287 K / Method: vapor diffusion, hanging drop / pH: 8
Details: MEPEG 2000, 100mM EPPS, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 287K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F2 / Wavelength: 0.979070, 0.979259, 0.994904
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 25, 2002
RadiationMonochromator: Si 111 CHANNEL / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.979071
20.9792591
30.9949041
ReflectionResolution: 1.7→55 Å / Num. obs: 35921 / % possible obs: 99 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 4 % / Rmerge(I) obs: 0.035 / Net I/σ(I): 20.4
Reflection shellResolution: 1.8→1.9 Å / Redundancy: 2.5 % / Mean I/σ(I) obs: 3 / Num. unique all: 3145 / Rsym value: 0.256 / % possible all: 99

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
CNSrefinement
RefinementMethod to determine structure: MAD / Resolution: 1.8→28.6 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
Details: THE R-FACTOR THAT WAS CALCULATED USING SFCHECK (0.388) IS MUCH GREATER THAN THAT REPORTED BY THE AUTHOR (0.199). THE REASON FOR THIS DISCREPANCY IS THAT SOME RESIDUES, DUE TO LACK OF ...Details: THE R-FACTOR THAT WAS CALCULATED USING SFCHECK (0.388) IS MUCH GREATER THAN THAT REPORTED BY THE AUTHOR (0.199). THE REASON FOR THIS DISCREPANCY IS THAT SOME RESIDUES, DUE TO LACK OF ELECTRON DENSITY, WERE MODELED AS ALANINE AND THE SIDE CHAINS WERE LATER ADDED AFTER REFINEMENT IN ORDER TO ACCOMODATE THE DEPOSITION.
RfactorNum. reflection% reflectionSelection details
Rfree0.23 5474 -Random 8%
Rwork0.199 ---
all0.199 ---
obs0.199 35879 88 %-
Refine analyzeLuzzati coordinate error obs: 0.23 Å / Luzzati d res low obs: 5 Å / Luzzati sigma a obs: 0.28 Å
Refinement stepCycle: LAST / Resolution: 1.8→28.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2660 0 0 252 2912
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_dihedral_angle_d24.9
X-RAY DIFFRACTIONc_improper_angle_d0.85
LS refinement shellResolution: 1.8→1.9 Å /
RfactorNum. reflection
Rfree0.31 434
Rwork0.29 -
obs-4983

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