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- PDB-1xkj: BACTERIAL LUCIFERASE BETA2 HOMODIMER -

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Basic information

Entry
Database: PDB / ID: 1xkj
TitleBACTERIAL LUCIFERASE BETA2 HOMODIMER
ComponentsBETA2 LUCIFERASE
KeywordsLUMINESCENCE / LUCIFERASE / PHOTOPROTEIN / OXIDOREDUCTASE
Function / homology
Function and homology information


bacterial luciferase / alkanal monooxygenase (FMN-linked) activity / bioluminescence / cytosol
Similarity search - Function
Alkanal monooxygenase / Bacterial luciferase, conserved site / Bacterial luciferase subunits signature. / Bacterial luciferase/NFP / Luciferase-like domain / Luciferase-like domain / Luciferase-like monooxygenase / Luciferase-like domain superfamily / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
Alkanal monooxygenase beta chain
Similarity search - Component
Biological speciesVibrio harveyi (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsTanner, J.J. / Krause, K.L.
CitationJournal: Biochemistry / Year: 1997
Title: Structure of bacterial luciferase beta 2 homodimer: implications for flavin binding.
Authors: Tanner, J.J. / Miller, M.D. / Wilson, K.S. / Tu, S.C. / Krause, K.L.
History
DepositionOct 8, 1996Processing site: BNL
Revision 1.0Jul 7, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 9, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: database_2 / diffrn_source ...database_2 / diffrn_source / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _pdbx_database_status.process_site
Revision 1.4May 22, 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: BETA2 LUCIFERASE
B: BETA2 LUCIFERASE


Theoretical massNumber of molelcules
Total (without water)72,7692
Polymers72,7692
Non-polymers00
Water55831
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3620 Å2
ΔGint-25 kcal/mol
Surface area26040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)112.400, 112.400, 153.700
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.756074, 0.000164, 0.654486), (-0.004306, -0.999977, 0.005225), (0.654472, -0.006768, -0.756056)
Vector: 8.1773, 77.4131, -21.6113)

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Components

#1: Protein BETA2 LUCIFERASE


Mass: 36384.684 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio harveyi (bacteria) / Gene: VIBRIO HARVEYI LUXAB / Plasmid: PTH3 / Gene (production host): VIBRIO HARVEYI LUXAB / Production host: Escherichia coli (E. coli) / Strain (production host): JM101 / References: UniProt: P07739, bacterial luciferase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 31 / 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: 2

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Sample preparation

CrystalDensity Matthews: 3.5 Å3/Da / Density % sol: 64 % / Description: DATA MERGED FROM TWO CRYSTALS
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.2
Details: SITTING DROP, 277 KELVIN, 12% PEG 4000, 17-21% ISOPROPANOL, 0.006M DTT, 0.1M CITRATE PH 6.2. 50 MG/ML PROTEIN., vapor diffusion - sitting drop
Crystal grow
*PLUS
Temperature: 4 ℃ / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
112 %PEG40001reservoir
217-21 %2-propanol1reservoir
36 mMDTT1reservoir
40.1 Mcitrate1reservoir

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7B / Wavelength: 0.865
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Oct 6, 1994
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.865 Å / Relative weight: 1
ReflectionResolution: 2.5→15 Å / Num. obs: 32225 / % possible obs: 93 % / Redundancy: 8 % / Biso Wilson estimate: 32.1 Å2 / Rmerge(I) obs: 0.088
Reflection
*PLUS
Num. measured all: 245416
Reflection shell
*PLUS
Highest resolution: 2.5 Å / Lowest resolution: 2.6 Å / % possible obs: 78 %

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Processing

Software
NameVersionClassification
X-PLOR3.843model building
X-PLOR3.843refinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLOR3.843phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: LUCIFERASE AB HETERODIMER (PDB ENTRY 1BRL)

1brl


Resolution: 2.5→15 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.001 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.249 3249 10.1 %RANDOM
Rwork0.191 ---
obs0.191 32225 93.3 %-
Displacement parametersBiso mean: 37.8 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.36 Å0.29 Å
Luzzati d res low-5 Å
Luzzati sigma a0.42 Å0.37 Å
Refinement stepCycle: LAST / Resolution: 2.5→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5061 0 0 31 5092
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.013
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.6
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d23.3
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.4
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it1.821
X-RAY DIFFRACTIONx_mcangle_it3.141.5
X-RAY DIFFRACTIONx_scbond_it3.291.5
X-RAY DIFFRACTIONx_scangle_it5.392
LS refinement shellResolution: 2.5→2.66 Å / Rfactor Rfree error: 0.017 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.354 442 9.8 %
Rwork0.313 4057 -
obs--79.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2PARAM11.WATTOPH11.WAT
Software
*PLUS
Name: X-PLOR / Version: 3.843 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg23.3
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.4

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