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

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Basic information

Entry
Database: PDB / ID: 2psf
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: 1.4 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: Advisory / 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 / 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
B: Renilla-luciferin 2-monooxygenase


Theoretical massNumber of molelcules
Total (without water)71,8862
Polymers71,8862
Non-polymers00
Water14,232790
1
A: Renilla-luciferin 2-monooxygenase


Theoretical massNumber of molelcules
Total (without water)35,9431
Polymers35,9431
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Renilla-luciferin 2-monooxygenase


Theoretical massNumber of molelcules
Total (without water)35,9431
Polymers35,9431
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)81.178, 82.279, 90.379
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 35943.059 Da / Num. of mol.: 2
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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 790 / 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: 2.1 Å3/Da / Density % sol: 41.38 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: 0.4M sodium acetate, 20% w/v PEG 3350, 1.8mM n-Decyl-beta-D-thiomaltoside, 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: Sep 17, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 1.4→50 Å / Num. obs: 111557 / 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: 1.4→50 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.957 / SU B: 1.98 / SU ML: 0.04 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.063 / ESU R Free: 0.063 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19406 5879 5 %RANDOM
Rwork0.17257 ---
obs0.17366 111557 98.32 %-
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: 15.561 Å2
Baniso -1Baniso -2Baniso -3
1-0.06 Å20 Å20 Å2
2---0.28 Å20 Å2
3---0.22 Å2
Refinement stepCycle: LAST / Resolution: 1.4→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4983 0 0 790 5773
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0225127
X-RAY DIFFRACTIONr_bond_other_d0.0010.023578
X-RAY DIFFRACTIONr_angle_refined_deg1.2091.9516942
X-RAY DIFFRACTIONr_angle_other_deg0.88238697
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5225606
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.56124.04250
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.16215898
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.8421528
X-RAY DIFFRACTIONr_chiral_restr0.0780.2723
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.025645
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021063
X-RAY DIFFRACTIONr_nbd_refined0.2130.21084
X-RAY DIFFRACTIONr_nbd_other0.1930.23870
X-RAY DIFFRACTIONr_nbtor_refined0.1840.22515
X-RAY DIFFRACTIONr_nbtor_other0.0830.22440
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1130.2552
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1260.27
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1860.238
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1070.248
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.711.53949
X-RAY DIFFRACTIONr_mcbond_other0.1211.51213
X-RAY DIFFRACTIONr_mcangle_it0.80724928
X-RAY DIFFRACTIONr_scbond_it1.58432514
X-RAY DIFFRACTIONr_scangle_it2.1594.52014
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.4→1.436 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.289 406 -
Rwork0.28 7585 -
obs--91.47 %
Refinement TLS params.

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

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.5407-0.09270.04290.92460.19691.25080.02110.01050.04750.01130.0046-0.0319-0.110.0357-0.0258-0.11850.00660.0076-0.13060.0072-0.122938.706210.713510.674
20.86530.2394-0.00181.4255-0.00271.2525-0.0112-0.0082-0.13980.03860.0439-0.08380.12350.0184-0.0327-0.11950.0062-0.0064-0.1257-0.0044-0.109336.8687-24.945-12.8322
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA3 - 3092 - 308
2X-RAY DIFFRACTION2BB10 - 3109 - 309

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