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- PDB-3fgc: Crystal Structure of the Bacterial Luciferase:Flavin Complex Reve... -

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Basic information

Entry
Database: PDB / ID: 3fgc
TitleCrystal Structure of the Bacterial Luciferase:Flavin Complex Reveals the Basis of Intersubunit Communication
Components(Alkanal monooxygenase ...) x 2
KeywordsOXIDOREDUCTASE / FMN bacterial luciferase mobile loop / Flavoprotein / FMN / Luminescence / Monooxygenase / Photoprotein
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 ...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
FLAVIN MONONUCLEOTIDE / PHOSPHATE ION / Alkanal monooxygenase beta chain / Alkanal monooxygenase alpha chain
Similarity search - Component
Biological speciesVibrio harveyi (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsCampbell, Z.T. / Weichsel, A. / Montfort, W.R. / Baldwin, T.O.
CitationJournal: Biochemistry / Year: 2009
Title: Crystal structure of the bacterial luciferase/flavin complex provides insight into the function of the beta subunit.
Authors: Campbell, Z.T. / Weichsel, A. / Montfort, W.R. / Baldwin, T.O.
History
DepositionDec 5, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 26, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
Revision 1.3Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Alkanal monooxygenase alpha chain
B: Alkanal monooxygenase beta chain
C: Alkanal monooxygenase alpha chain
D: Alkanal monooxygenase beta chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)157,48923
Polymers155,3064
Non-polymers2,18319
Water14,070781
1
A: Alkanal monooxygenase alpha chain
B: Alkanal monooxygenase beta chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,97312
Polymers77,6532
Non-polymers1,32010
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7530 Å2
ΔGint-157 kcal/mol
Surface area26090 Å2
MethodPISA
2
C: Alkanal monooxygenase alpha chain
D: Alkanal monooxygenase beta chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,51611
Polymers77,6532
Non-polymers8639
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6120 Å2
ΔGint-108 kcal/mol
Surface area26270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.886, 109.301, 301.419
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Alkanal monooxygenase ... , 2 types, 4 molecules ACBD

#1: Protein Alkanal monooxygenase alpha chain / Bacterial luciferase alpha chain


Mass: 40197.062 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio harveyi (bacteria) / Gene: luxA / Plasmid: pET21-b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P07740, bacterial luciferase
#2: Protein Alkanal monooxygenase beta chain / Bacterial luciferase beta chain


Mass: 37455.824 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio harveyi (bacteria) / Gene: luxB / Plasmid: pET21-b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P07739, bacterial luciferase

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Non-polymers , 4 types, 800 molecules

#3: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE


Mass: 456.344 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H21N4O9P
#4: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#5: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 781 / 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: 3.12 Å3/Da / Density % sol: 60.61 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 100 mM Na+/K+ phosphate pH 7.5 and 1.65 M ammonium sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-1 / Wavelength: 0.9 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Feb 4, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2.3→27.33 Å / Num. all: 83087 / Num. obs: 83194 / % possible obs: 99.9 % / Redundancy: 11.1 % / Biso Wilson estimate: 26.842 Å2 / Rmerge(I) obs: 0.429 / Rsym value: 0.096 / Net I/σ(I): 43.3
Reflection shellResolution: 2.3→2.36 Å / Rmerge(I) obs: 0.204 / Rsym value: 0.287 / % possible all: 99.08

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
REFMAC5.2.0019refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1LUC

1luc


Resolution: 2.3→27.33 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.908 / SU B: 5.495 / SU ML: 0.137 / Cross valid method: THROUGHOUT / ESU R: 0.25 / ESU R Free: 0.214 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24087 4385 5 %RANDOM
Rwork0.1839 ---
all0.18676 ---
obs0.18672 83087 99.87 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 26.842 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2.3→27.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10927 0 121 847 11895
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.02211341
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6811.94315423
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8251409
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.87924.838587
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.315151869
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.2951554
X-RAY DIFFRACTIONr_chiral_restr0.1170.21633
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.028847
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2090.25394
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3050.27723
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1540.2858
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.190.270
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2060.233
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.0841.57129
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.662211089
X-RAY DIFFRACTIONr_scbond_it2.834939
X-RAY DIFFRACTIONr_scangle_it4.0944.54331
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.287 334 -
Rwork0.204 5990 -
obs--99.08 %

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