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

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Basic information

Entry
Database: PDB / ID: 2psh
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 / carboxy-lyase activity / bioluminescence / membrane
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
Coelenterazine h 2-monooxygenase
Similarity search - Component
Biological speciesRenilla reniformis (sea pansy)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.79 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 1.0Jun 5, 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 / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Feb 21, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Renilla-luciferin 2-monooxygenase
B: Renilla-luciferin 2-monooxygenase


Theoretical massNumber of molelcules
Total (without water)74,0302
Polymers74,0302
Non-polymers00
Water8,575476
1
A: Renilla-luciferin 2-monooxygenase


Theoretical massNumber of molelcules
Total (without water)37,0151
Polymers37,0151
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Renilla-luciferin 2-monooxygenase


Theoretical massNumber of molelcules
Total (without water)37,0151
Polymers37,0151
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)51.776, 75.652, 89.185
Angle α, β, γ (deg.)90.00, 76.48, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: SER / Beg label comp-ID: SER / End auth comp-ID: GLU / End label comp-ID: GLU / Refine code: 4 / Auth seq-ID: 3 - 310 / Label seq-ID: 3 - 310

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

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


Mass: 37015.230 Da / Num. of mol.: 2
Mutation: T2A, K25A, A55T, C124A, S130A, K136R, A143M, M185V, M253L, E277A, 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 476 / 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: 2.29 Å3/Da / Density % sol: 46.36 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1~M HEPES, 10% v/v isopropanol with 6mg/ml benzyl-coelenterazine, 15% w/v PEG 3350, pH 7.5, 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
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 1.79→100 Å / Num. obs: 58344 / 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: 1.79→86.71 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.934 / SU B: 2.928 / SU ML: 0.091 / Cross valid method: THROUGHOUT / ESU R: 0.136 / ESU R Free: 0.127 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22941 3119 5.1 %RANDOM
Rwork0.19523 ---
obs0.19698 58344 97.55 %-
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: 18.086 Å2
Baniso -1Baniso -2Baniso -3
1-0.95 Å20 Å20.04 Å2
2--0.13 Å20 Å2
3----1.1 Å2
Refinement stepCycle: LAST / Resolution: 1.79→86.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4860 0 0 476 5336
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0224994
X-RAY DIFFRACTIONr_bond_other_d0.0010.023487
X-RAY DIFFRACTIONr_angle_refined_deg1.2121.9526755
X-RAY DIFFRACTIONr_angle_other_deg0.87838473
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6425593
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.84323.824238
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.78415872
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.8971528
X-RAY DIFFRACTIONr_chiral_restr0.0770.2710
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.025483
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021040
X-RAY DIFFRACTIONr_nbd_refined0.2120.21072
X-RAY DIFFRACTIONr_nbd_other0.1930.23548
X-RAY DIFFRACTIONr_nbtor_refined0.1790.22446
X-RAY DIFFRACTIONr_nbtor_other0.0820.22337
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1250.2379
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1390.22
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1690.223
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1160.228
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.7761.53864
X-RAY DIFFRACTIONr_mcbond_other0.1221.51192
X-RAY DIFFRACTIONr_mcangle_it0.85824821
X-RAY DIFFRACTIONr_scbond_it1.39532434
X-RAY DIFFRACTIONr_scangle_it1.9944.51934
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 4149 / Refine-ID: X-RAY DIFFRACTION / Rms dev position: 0.42 Å

TypeWeight position
medium positional0.5
medium thermal2
LS refinement shellResolution: 1.79→1.837 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.353 201 -
Rwork0.298 3552 -
obs--80.69 %

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