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- PDB-2pse: Crystal Structures of the Luciferase and Green Fluorescent Protei... -

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Basic information

Entry
Database: PDB / ID: 2pse
TitleCrystal Structures of the Luciferase and Green Fluorescent Protein from Renilla Reniformis
ComponentsRenilla-luciferin 2-monooxygenase
KeywordsOXIDOREDUCTASE / alpha/beta-hydrolase / luciferase
Function / homology
Function and homology information


Renilla-type luciferase / Renilla-luciferin 2-monooxygenase activity / epoxide hydrolase activity / carboxy-lyase activity / bioluminescence
Similarity search - Function
Epoxide hydrolase-like / alpha/beta hydrolase fold / Alpha/beta hydrolase fold-1 / Alpha/Beta hydrolase fold, catalytic domain / Alpha/Beta hydrolase fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
IMIDAZOLE / Coelenterazine h 2-monooxygenase
Similarity search - Component
Biological speciesRenilla reniformis (sea pansy)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsLoening, A.M. / Fenn, T.D. / Gambhir, S.S.
CitationJournal: J.Mol.Biol. / Year: 2007
Title: Crystal Structures of the Luciferase and Green Fluorescent Protein from Renilla reniformis.
Authors: Loening, A.M. / Fenn, T.D. / Gambhir, S.S.
History
DepositionMay 6, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 22, 2007Provider: repository / Type: Initial release
Revision 1.1Nov 19, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 20, 2021Group: Database references / Derived calculations / Category: database_2 / 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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Feb 21, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Renilla-luciferin 2-monooxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,0692
Polymers37,0001
Non-polymers691
Water1,36976
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)119.443, 119.443, 48.048
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61

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Components

#1: Protein Renilla-luciferin 2-monooxygenase / Renilla-type luciferase


Mass: 37000.172 Da / Num. of mol.: 1
Mutation: A55T, C124A, S130A, K136R, A143M, M185V, M253L, S287L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Renilla reniformis (sea pansy) / Gene: rluc / Plasmid: pBAD / Production host: Escherichia coli (E. coli) / Strain (production host): LMG194 / References: UniProt: P27652, Renilla-type luciferase
#2: Chemical ChemComp-IMD / IMIDAZOLE


Mass: 69.085 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H5N2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 76 / 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: 2.67 Å3/Da / Density % sol: 53.98 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: 0.15 KSCN, 15% w/v PEG 6000, 0.1 M Tris-HCl, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2
DetectorDate: May 17, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.5→50 Å / Num. obs: 11477 / Observed criterion σ(F): 0 / Observed criterion σ(I): 0

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Processing

SoftwareName: REFMAC / Version: 5.2.0019 / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→43.56 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.916 / SU B: 9.232 / SU ML: 0.202 / Cross valid method: THROUGHOUT / ESU R: 0.76 / ESU R Free: 0.291 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23248 604 5 %RANDOM
Rwork0.1913 ---
obs0.19344 11477 89.22 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 29.204 Å2
Baniso -1Baniso -2Baniso -3
1-0.53 Å20.26 Å20 Å2
2--0.53 Å20 Å2
3----0.79 Å2
Refinement stepCycle: LAST / Resolution: 2.5→43.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2502 0 5 76 2583
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0222580
X-RAY DIFFRACTIONr_bond_other_d0.0020.021804
X-RAY DIFFRACTIONr_angle_refined_deg1.5881.9543492
X-RAY DIFFRACTIONr_angle_other_deg0.95734383
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7445304
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.87524125
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.59115451
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.541514
X-RAY DIFFRACTIONr_chiral_restr0.0890.2363
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022837
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02539
X-RAY DIFFRACTIONr_nbd_refined0.2280.2627
X-RAY DIFFRACTIONr_nbd_other0.2050.21944
X-RAY DIFFRACTIONr_nbtor_refined0.1940.21258
X-RAY DIFFRACTIONr_nbtor_other0.0930.21272
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.190.2110
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1470.25
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3390.224
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1350.25
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.8361.51953
X-RAY DIFFRACTIONr_mcbond_other0.1391.5608
X-RAY DIFFRACTIONr_mcangle_it1.06122474
X-RAY DIFFRACTIONr_scbond_it1.66231267
X-RAY DIFFRACTIONr_scangle_it2.4254.51018
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.5→2.564 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.409 34 -
Rwork0.309 727 -
obs--77.57 %

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