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- PDB-2isl: BluB bound to reduced flavin (FMNH2) and molecular oxygen. (clear... -

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Basic information

Entry
Database: PDB / ID: 2isl
TitleBluB bound to reduced flavin (FMNH2) and molecular oxygen. (clear crystal form)
ComponentsBluB
KeywordsFLAVOPROTEIN / flavin / oxidoreductase / monooxygenase / flavin destructase / molecular oxygen
Function / homology
Function and homology information


aerobic 5,6-dimethylbenzimidazole synthase / 5,6-dimethylbenzimidazole synthase activity / cobalamin biosynthetic process / oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen / nucleotide binding
Similarity search - Function
5,6-dimethylbenzimidazole synthase BluB / : / NADH Oxidase / NADH Oxidase / Nitroreductase / Nitroreductase family / Nitroreductase-like / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-FNR / OXYGEN MOLECULE / 5,6-dimethylbenzimidazole synthase
Similarity search - Component
Biological speciesSinorhizobium meliloti (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsLarsen, N.A. / Taga, M.E. / Howard-Jones, A.R. / Walsh, C.T. / Walker, G.C.
Citation
Journal: Nature / Year: 2007
Title: BluB cannibalizes flavin to form the lower ligand of vitamin B12.
Authors: Taga, M.E. / Larsen, N.A. / Howard-Jones, A.R. / Walsh, C.T. / Walker, G.C.
#1: Journal: Proc.Natl.Acad.Sci.USA / Year: 2006
Title: Sinorhizobium meliloti bluB is necessary for production of 5,6-dimethylbenzimidazole, the lower ligand of B12.
History
DepositionOct 17, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 27, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: BluB
B: BluB
C: BluB
D: BluB
E: BluB
F: BluB
G: BluB
H: BluB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)210,48624
Polymers206,5638
Non-polymers3,92316
Water1,13563
1
A: BluB
B: BluB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,6216
Polymers51,6412
Non-polymers9814
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11810 Å2
ΔGint-66 kcal/mol
Surface area15840 Å2
MethodPISA
2
C: BluB
D: BluB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,6216
Polymers51,6412
Non-polymers9814
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11790 Å2
ΔGint-66 kcal/mol
Surface area15960 Å2
MethodPISA
3
E: BluB
F: BluB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,6216
Polymers51,6412
Non-polymers9814
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11740 Å2
ΔGint-70 kcal/mol
Surface area15980 Å2
MethodPISA
4
G: BluB
H: BluB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,6216
Polymers51,6412
Non-polymers9814
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11830 Å2
ΔGint-71 kcal/mol
Surface area15760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.073, 173.836, 91.977
Angle α, β, γ (deg.)90.00, 89.96, 90.00
Int Tables number4
Space group name H-MP1211
DetailsThe biological assembly consists of a homodimer. There are 4 dimers in the asymmetric unit. Dimer1 = chain A/B, Dimer2 = chain C/D, Dimer3 = chain E/F, Dimer4 = chain G/H

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Components

#1: Protein
BluB


Mass: 25820.369 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sinorhizobium meliloti (bacteria) / Gene: bluB / Plasmid: pET-28b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: Q92PC8
#2: Chemical
ChemComp-FNR / 1-DEOXY-1-(7,8-DIMETHYL-2,4-DIOXO-3,4-DIHYDRO-2H-BENZO[G]PTERIDIN-1-ID-10(5H)-YL)-5-O-PHOSPHONATO-D-RIBITOL / TWO ELECTRON REDUCED FLAVIN MONONUCLEOTIDE


Mass: 458.360 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C17H23N4O9P
#3: Chemical
ChemComp-OXY / OXYGEN MOLECULE


Mass: 31.999 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 63 / 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: 2.52 Å3/Da / Density % sol: 51.14 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 0.8 Ammonium Sulfate, 100 mM citrate soaked in saturated dithionite, and then backsoaked in oxygenated mother liquor prior to freezing, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 0.9919 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 2, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9919 Å / Relative weight: 1
ReflectionResolution: 2.9→50 Å / Num. all: 44966 / Num. obs: 44966 / % possible obs: 100 % / Observed criterion σ(F): 3.3 / Observed criterion σ(I): 3.3 / Redundancy: 3.8 % / Rmerge(I) obs: 0.079 / Net I/σ(I): 15.1
Reflection shellResolution: 2.9→3 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.315 / Mean I/σ(I) obs: 3.3 / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-2000data collection
MOLREPphasing
CNS1.1refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.9→20 Å / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.285 2170 -random
Rwork0.217 ---
all0.22 44966 --
obs0.22 43289 95.7 %-
Displacement parametersBiso mean: 36 Å2
Baniso -1Baniso -2Baniso -3
1--3.672 Å20 Å20 Å2
2--0.127 Å20 Å2
3---3.545 Å2
Refinement stepCycle: LAST / Resolution: 2.9→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13928 0 264 63 14255
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONo_bond_d
X-RAY DIFFRACTIONo_bond_d_na
X-RAY DIFFRACTIONo_bond_d_prot
X-RAY DIFFRACTIONo_angle_d
X-RAY DIFFRACTIONo_angle_d_na
X-RAY DIFFRACTIONo_angle_d_prot
X-RAY DIFFRACTIONo_angle_deg
X-RAY DIFFRACTIONo_angle_deg_na
X-RAY DIFFRACTIONo_angle_deg_prot
X-RAY DIFFRACTIONo_dihedral_angle_d
X-RAY DIFFRACTIONo_dihedral_angle_d_na
X-RAY DIFFRACTIONo_dihedral_angle_d_prot
X-RAY DIFFRACTIONo_improper_angle_d
X-RAY DIFFRACTIONo_improper_angle_d_na
X-RAY DIFFRACTIONo_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.2641.5
X-RAY DIFFRACTIONc_mcangle_it2.1992
X-RAY DIFFRACTIONc_scbond_it1.6062
X-RAY DIFFRACTIONc_scangle_it2.4752.5
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1protein_rep.param
X-RAY DIFFRACTION2water_rep.param
X-RAY DIFFRACTION3fmnh2.par
X-RAY DIFFRACTION4oxy.param

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