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- PDB-2isj: BluB bound to oxidized FMN -

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ID or keywords:

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Basic information

Entry
Database: PDB / ID: 2isj
TitleBluB bound to oxidized FMN
ComponentsBluB
KeywordsFLAVOPROTEIN / oxidoreductase / flavin / monooxygenase / flavin destructase / vitamin b12
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
FLAVIN MONONUCLEOTIDE / 5,6-dimethylbenzimidazole synthase
Similarity search - Component
Biological speciesSinorhizobium meliloti (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 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-dimethlybenzimidazole, 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)210,21416
Polymers206,5638
Non-polymers3,6518
Water9,350519
1
A: BluB
B: BluB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,5534
Polymers51,6412
Non-polymers9132
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11640 Å2
ΔGint-70 kcal/mol
Surface area15910 Å2
MethodPISA
2
C: BluB
D: BluB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,5534
Polymers51,6412
Non-polymers9132
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11660 Å2
ΔGint-73 kcal/mol
Surface area15840 Å2
MethodPISA
3
E: BluB
F: BluB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,5534
Polymers51,6412
Non-polymers9132
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11690 Å2
ΔGint-68 kcal/mol
Surface area15940 Å2
MethodPISA
4
G: BluB
H: BluB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,5534
Polymers51,6412
Non-polymers9132
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11730 Å2
ΔGint-72 kcal/mol
Surface area15930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.149, 172.724, 92.063
Angle α, β, γ (deg.)90.00, 90.06, 90.00
Int Tables number4
Space group name H-MP1211
DetailsThe biological unit is a homodimer. There are 4 homodimers in the assymetric unit. Dimer 1: chain A and B, Dimer 2: chain C and D, Dimer 3: chain E and F, Dimer 4: chain G and 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-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE


Mass: 456.344 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C17H21N4O9P
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 519 / 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: 2.51 Å3/Da / Density % sol: 50.93 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 0.8 M Ammonium Sulfate, 100 mM citrate, 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: 2.3→50 Å / Num. all: 81156 / Num. obs: 81156 / % possible obs: 90.2 % / Observed criterion σ(F): 3.3 / Observed criterion σ(I): 3.3 / Redundancy: 2.8 % / Rsym value: 0.069 / Net I/σ(I): 10.7
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.194 / Mean I/σ(I) obs: 3.3 / % possible all: 91.8

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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: 2.3→50 Å / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.252 3618 -random
Rwork0.207 ---
all0.218 79929 --
obs0.21 71996 80 %-
Displacement parametersBiso mean: 21 Å2
Baniso -1Baniso -2Baniso -3
1--0.065 Å20 Å20 Å2
2---0.964 Å20 Å2
3---1.029 Å2
Refinement stepCycle: LAST / Resolution: 2.3→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13928 0 248 519 14695
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_it1.1921.5
X-RAY DIFFRACTIONc_mcangle_it1.8682
X-RAY DIFFRACTIONc_scbond_it1.8292
X-RAY DIFFRACTIONc_scangle_it2.6052.5
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1protein_rep.param
X-RAY DIFFRACTION2water_rep.param
X-RAY DIFFRACTION3fmn2.par

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