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- PDB-1bsl: STRUCTURE OF ALKANAL MONOOXYGENASE BETA CHAIN -

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Basic information

Entry
Database: PDB / ID: 1bsl
TitleSTRUCTURE OF ALKANAL MONOOXYGENASE BETA CHAIN
ComponentsBACTERIAL LUCIFERASE
KeywordsFLAVOPROTEIN / PHOTOPROTEIN / LUMINESCENCE / OXIDOREDUCTASE / MONOOXYGENASE / FMN
Function / homology
Function and homology information


bacterial luciferase / alkanal monooxygenase (FMN-linked) activity / bioluminescence
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 / Resolution: 1.95 Å
AuthorsRayment, I. / Holden, H.M. / Thoden, J.B. / Baldwin, T.O.
Citation
Journal: Protein Sci. / Year: 1997
Title: Structure of the beta 2 homodimer of bacterial luciferase from Vibrio harveyi: X-ray analysis of a kinetic protein folding trap.
Authors: Thoden, J.B. / Holden, H.M. / Fisher, A.J. / Sinclair, J.F. / Wesenberg, G. / Baldwin, T.O. / Rayment, I.
#1: Journal: J.Biol.Chem. / Year: 1996
Title: The 1.5-A Resolution Crystal Structure of Bacterial Luciferase in Low Salt Conditions
Authors: Fisher, A.J. / Thompson, T.B. / Thoden, J.B. / Baldwin, T.O. / Rayment, I.
History
DepositionOct 22, 1996Processing site: BNL
Revision 1.0Nov 12, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: BACTERIAL LUCIFERASE
B: BACTERIAL LUCIFERASE


Theoretical massNumber of molelcules
Total (without water)72,7692
Polymers72,7692
Non-polymers00
Water17,817989
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3790 Å2
ΔGint-24 kcal/mol
Surface area25450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.800, 62.000, 218.200
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 BACTERIAL LUCIFERASE


Mass: 36384.684 Da / Num. of mol.: 2 / Fragment: BETA SUBUNIT
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio harveyi (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: P07739, bacterial luciferase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 989 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.73 Å3/Da / Density % sol: 54.98 %
Crystal grow
*PLUS
pH: 7 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
110-12.5 mg/mlprotein1drop
250 mMphosphate1drop
30.5 mMEDTA1drop
40.25 mMdithiothreitol1drop
50.75 Mammonium sulfate1drop
6125 mMsodium borate1drop
725 mMsuccinic1drop
81.5 Mammonium sulfate1reservoir

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Data collection

Diffraction sourceWavelength: 1.5418
DetectorType: SIEMENS / Detector: AREA DETECTOR / Date: Jun 1, 1995
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionNum. obs: 55442 / % possible obs: 93.7 % / Redundancy: 2.2 % / Rmerge(I) obs: 0.041
Reflection
*PLUS
Highest resolution: 1.95 Å / Lowest resolution: 30 Å / Num. measured all: 125700
Reflection shell
*PLUS
Highest resolution: 1.95 Å / % possible obs: 85.1 % / Num. unique obs: 6873 / Num. measured obs: 9563 / Rmerge(I) obs: 0.18

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Processing

Software
NameClassification
TNTrefinement
XDSdata reduction
RefinementResolution: 1.95→30 Å /
RfactorNum. reflection
Rwork0.188 -
obs-55442
Refinement stepCycle: LAST / Resolution: 1.95→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5127 0 0 989 6116
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_bond_d0.016
X-RAY DIFFRACTIONt_angle_deg2.5
X-RAY DIFFRACTIONt_dihedral_angle_d
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes
X-RAY DIFFRACTIONt_it
X-RAY DIFFRACTIONt_nbd
Software
*PLUS
Name: TNT / Classification: refinement
Refinement
*PLUS
Rfactor all: 0.188
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_deg16.9
X-RAY DIFFRACTIONt_planar_d0.007
X-RAY DIFFRACTIONt_plane_restr0.012

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