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Basic information

Entry
Database: PDB / ID: 2psj
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
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
Chem-CEI / Coelenterazine h 2-monooxygenase
Similarity search - Component
Biological speciesRenilla reniformis (sea pansy)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 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: Advisory / 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 / 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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)75,0864
Polymers74,2632
Non-polymers8232
Water8,161453
1
A: Renilla-luciferin 2-monooxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,5432
Polymers37,1311
Non-polymers4111
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Renilla-luciferin 2-monooxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,5432
Polymers37,1311
Non-polymers4111
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)51.329, 74.473, 89.249
Angle α, β, γ (deg.)90.00, 103.45, 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: 37131.367 Da / Num. of mol.: 2
Mutation: T2A, 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-CEI / N-[3-BENZYL-5-(4-HYDROXYPHENYL)PYRAZIN-2-YL]-2-(4-HYDROXYPHENYL)ACETAMIDE / COELENTERAMIDE / Coelenteramide


Mass: 411.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C25H21N3O3
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 453 / 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: 2.23 Å3/Da / Density % sol: 44.91 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1M HEPES, 10% v/v isopropanol with 6mg/ml 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: 1.8→50 Å / Num. obs: 55608 / 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: 1.8→50 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.939 / SU B: 5.418 / SU ML: 0.087 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.141 / ESU R Free: 0.126 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21597 2915 5 %RANDOM
Rwork0.18755 ---
obs0.18898 55608 96.44 %-
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: 21.443 Å2
Baniso -1Baniso -2Baniso -3
1-1.09 Å20 Å2-0.31 Å2
2---0.66 Å20 Å2
3----0.57 Å2
Refinement stepCycle: LAST / Resolution: 1.8→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5006 0 62 453 5521
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0225214
X-RAY DIFFRACTIONr_bond_other_d0.0010.023634
X-RAY DIFFRACTIONr_angle_refined_deg1.1941.9687054
X-RAY DIFFRACTIONr_angle_other_deg0.8638826
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6245608
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.26624.08250
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.03915906
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.7471528
X-RAY DIFFRACTIONr_chiral_restr0.0740.2728
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.025726
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021086
X-RAY DIFFRACTIONr_nbd_refined0.2090.21116
X-RAY DIFFRACTIONr_nbd_other0.1930.23817
X-RAY DIFFRACTIONr_nbtor_refined0.1840.22554
X-RAY DIFFRACTIONr_nbtor_other0.0830.22460
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1350.2397
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1360.217
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1240.242
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1480.225
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.6421.53975
X-RAY DIFFRACTIONr_mcbond_other0.121.51220
X-RAY DIFFRACTIONr_mcangle_it0.70824958
X-RAY DIFFRACTIONr_scbond_it1.33132621
X-RAY DIFFRACTIONr_scangle_it1.9284.52096
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: 4303 / Refine-ID: X-RAY DIFFRACTION

TypeRms dev position (Å)Weight position
medium positional0.120.5
medium thermal0.32
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.299 183 -
Rwork0.265 3976 -
obs--92.22 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
10.61880.0544-0.0081.64130.50031.91070.0415-0.04030.03760.0015-0.01080.0445-0.0537-0.0254-0.0307-0.1318-0.00570.0049-0.114-0.0003-0.1189-1.1074-10.062538.7146
20.8763-0.2278-0.27861.51290.081.55620.00270.0634-0.0285-0.07590.00670.03470.0373-0.0085-0.0094-0.13470.0109-0.0141-0.1238-0.0062-0.13356.0839-39.94028.813
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA3 - 3093 - 309
2X-RAY DIFFRACTION1AC5011
3X-RAY DIFFRACTION2BB10 - 31010 - 310
4X-RAY DIFFRACTION2BD5021

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