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

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Basic information

Entry
Database: PDB / ID: 2psd
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: 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 1.0Jun 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 / 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)37,1383
Polymers37,0001
Non-polymers1382
Water6,918384
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)119.468, 119.468, 47.995
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.: 2 / Source method: obtained synthetically / Formula: C3H5N2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 384 / 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: 53.95 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 0.3M NaCl, 1.25M diammonium phosphate, 0.1M imidazole, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 1.4→50 Å / Num. obs: 73121 / Observed criterion σ(F): 0 / Observed criterion σ(I): 0

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Processing

SoftwareName: REFMAC / Version: 5.2.0005 / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.4→50 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.97 / SU B: 2.178 / SU ML: 0.042 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.051 / ESU R Free: 0.052 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18341 3868 5 %RANDOM
Rwork0.16539 ---
obs0.16631 73121 99.82 %-
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: 21.001 Å2
Baniso -1Baniso -2Baniso -3
1-0.51 Å20.25 Å20 Å2
2--0.51 Å20 Å2
3----0.76 Å2
Refinement stepCycle: LAST / Resolution: 1.4→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2502 0 10 384 2896
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0222610
X-RAY DIFFRACTIONr_bond_other_d0.0010.022344
X-RAY DIFFRACTIONr_angle_refined_deg1.3721.9563534
X-RAY DIFFRACTIONr_angle_other_deg0.84335474
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7995310
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.9924125
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.57415458
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.6151514
X-RAY DIFFRACTIONr_chiral_restr0.0930.2366
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022884
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02550
X-RAY DIFFRACTIONr_nbd_refined0.2150.2564
X-RAY DIFFRACTIONr_nbd_other0.1890.22494
X-RAY DIFFRACTIONr_nbtor_refined0.1890.21309
X-RAY DIFFRACTIONr_nbtor_other0.0820.21418
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1180.2272
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.0580.25
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2830.226
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1780.229
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.8021.52011
X-RAY DIFFRACTIONr_mcbond_other0.1671.5617
X-RAY DIFFRACTIONr_mcangle_it0.89122507
X-RAY DIFFRACTIONr_scbond_it1.74631277
X-RAY DIFFRACTIONr_scangle_it2.4684.51027
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
Rfree0.414 280 -
Rwork0.382 5261 -
obs--97.79 %
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)
10.91980.10180.53791.42970.08461.92630.10430.0341-0.03680.1166-0.0218-0.07460.11030.1128-0.0825-0.1423-0.0055-0.017-0.14210.0385-0.136182.39740.7371-0.3043
21.15530.10910.68850.75350.20473.52030.1027-0.1680.00520.1866-0.06070.20240.0561-0.6419-0.042-0.0975-0.01230.0411-0.00110.0393-0.082165.81875.49656.0514
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA4 - 1503 - 149
2X-RAY DIFFRACTION1AA226 - 308225 - 307
3X-RAY DIFFRACTION2AA151 - 225150 - 224

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