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- PDB-2b81: Crystal Structure of the Luciferase-like Monooxygenase from Bacil... -

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Basic information

Entry
Database: PDB / ID: 2b81
TitleCrystal Structure of the Luciferase-like Monooxygenase from Bacillus cereus
ComponentsLuciferase-like monooxygenase
KeywordsOXIDOREDUCTASE / TIM barrel / Structural Genomics / PSI / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG
Function / homology
Function and homology information


Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen / oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen / monooxygenase activity
Similarity search - Function
Luciferase-type oxidoreductase / : / Luciferase-like domain / Luciferase-like domain / Luciferase-like monooxygenase / Luciferase-like domain superfamily / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
Luciferase-like monooxygenase
Similarity search - Component
Biological speciesBacillus cereus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.5 Å
AuthorsKim, Y. / Li, H. / Moy, S. / Collart, F. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: Crystal Structure of the Luciferase-like Monooxygenase from Bacillus cereus
Authors: Kim, Y. / Li, H. / Moy, S. / Collart, F. / Joachimiak, A.
History
DepositionOct 6, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 22, 2005Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Oct 16, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / 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_conn.pdbx_leaving_atom_flag / _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: Luciferase-like monooxygenase
B: Luciferase-like monooxygenase
C: Luciferase-like monooxygenase
D: Luciferase-like monooxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)154,95553
Polymers149,7724
Non-polymers5,18349
Water18,8081044
1
A: Luciferase-like monooxygenase
B: Luciferase-like monooxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,47726
Polymers74,8862
Non-polymers2,59124
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9080 Å2
ΔGint-255 kcal/mol
Surface area24090 Å2
MethodPISA
2
C: Luciferase-like monooxygenase
D: Luciferase-like monooxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,47827
Polymers74,8862
Non-polymers2,59225
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8640 Å2
ΔGint-274 kcal/mol
Surface area24290 Å2
MethodPISA
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area20240 Å2
ΔGint-549 kcal/mol
Surface area45860 Å2
MethodPISA
4
C: Luciferase-like monooxygenase
D: Luciferase-like monooxygenase
hetero molecules

A: Luciferase-like monooxygenase
B: Luciferase-like monooxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)154,95553
Polymers149,7724
Non-polymers5,18349
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-x+1/2,-y+1,z+1/21
Buried area19060 Å2
ΔGint-546 kcal/mol
Surface area47040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)138.466, 159.942, 172.914
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
Luciferase-like monooxygenase


Mass: 37442.965 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus cereus (bacteria) / Plasmid: pMCSG7 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21DE3
References: UniProt: Q81B18, Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen
#2: Chemical...
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 39 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1044 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 6.8 Å3/Da / Density % sol: 82 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 6
Details: MES, ammonium sulfate, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97929 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 4, 2004 / Details: mirrors
RadiationMonochromator: double crystal monochromator, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97929 Å / Relative weight: 1
ReflectionResolution: 2.5→47.81 Å / Num. all: 131796 / Num. obs: 131719 / % possible obs: 99 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.6 % / Rmerge(I) obs: 0.14 / Net I/σ(I): 9.3
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 6.6 % / Rmerge(I) obs: 0.766 / Mean I/σ(I) obs: 3.4 / Num. unique all: 13005 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
SBC-Collectdata collection
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
HKL-3000phasing
SHELXDphasing
SOLVEphasing
RESOLVEphasing
MLPHAREphasing
RefinementMethod to determine structure: SAD / Resolution: 2.5→47.81 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.927 / SU B: 10.252 / SU ML: 0.12 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.197 / ESU R Free: 0.181 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: CNS was also used for the refinement.
RfactorNum. reflection% reflectionSelection details
Rfree0.21833 13183 10 %RANDOM
Rwork0.18261 ---
all0.18619 118322 --
obs0.18619 118322 99.46 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 35.05 Å2
Baniso -1Baniso -2Baniso -3
1--2.23 Å20 Å20 Å2
2--2.99 Å20 Å2
3----0.76 Å2
Refinement stepCycle: LAST / Resolution: 2.5→47.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10307 0 285 1044 11636
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.02211335
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3641.97915457
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.05551369
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.28423.948575
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.027151853
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.0951574
X-RAY DIFFRACTIONr_chiral_restr0.1010.21564
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.028882
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.210.25786
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3130.27653
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.150.21053
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2560.251
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1610.212
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.7591.56803
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.224210817
X-RAY DIFFRACTIONr_scbond_it1.88135045
X-RAY DIFFRACTIONr_scangle_it2.8024.54640
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.504→2.569 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.338 915 -
Rwork0.274 8233 -
obs-8233 94.63 %

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