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- PDB-3rgn: Crystal structure of spin-labeled BtuB W371R1 -

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Basic information

Entry
Database: PDB / ID: 3rgn
TitleCrystal structure of spin-labeled BtuB W371R1
ComponentsVitamin B12 transporter BtuB
KeywordsTRANSPORT PROTEIN / Beta-barrel / Receptor / Transporter / Cobalamins / TonB / Outer Membrane
Function / homology
Function and homology information


ABC-type vitamin B12 transporter activity / cobalamin transport / transmembrane transporter complex / porin activity / pore complex / monoatomic ion transmembrane transport / cell outer membrane / protein domain specific binding / calcium ion binding / membrane
Similarity search - Function
TonB-dependent vitamin B12 transporter BtuB / TonB-dependent receptor (TBDR) proteins signature 1. / TonB-dependent receptor, beta-barrel domain / TonB-dependent receptor, plug domain / Maltoporin; Chain A / TonB-dependent receptor (TBDR) proteins profile. / TonB box, conserved site / Ferric Hydroxamate Uptake Protein; Chain A, domain 1 / TonB-dependent receptor, conserved site / TonB-dependent receptor (TBDR) proteins signature 2. ...TonB-dependent vitamin B12 transporter BtuB / TonB-dependent receptor (TBDR) proteins signature 1. / TonB-dependent receptor, beta-barrel domain / TonB-dependent receptor, plug domain / Maltoporin; Chain A / TonB-dependent receptor (TBDR) proteins profile. / TonB box, conserved site / Ferric Hydroxamate Uptake Protein; Chain A, domain 1 / TonB-dependent receptor, conserved site / TonB-dependent receptor (TBDR) proteins signature 2. / Vitamin B12 transporter BtuB-like / TonB-dependent receptor-like, beta-barrel / TonB dependent receptor / TonB-dependent receptor, plug domain superfamily / TonB-dependent receptor, plug domain / TonB-dependent receptor-like, beta-barrel domain superfamily / TonB-dependent Receptor Plug Domain / Beta Complex / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Chem-MTN / Vitamin B12 transporter BtuB
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsFreed, D.M. / Horanyi, P.S. / Wiener, M.C. / Cafiso, D.S.
CitationJournal: Biochemistry / Year: 2011
Title: Molecular Origin of Electron Paramagnetic Resonance Line Shapes on β-Barrel Membrane Proteins: The Local Solvation Environment Modulates Spin-Label Configuration
Authors: Freed, D.M. / Khan, A.K. / Horanyi, P.S. / Cafiso, D.S.
History
DepositionApr 8, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 26, 2011Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software / Item: _software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Vitamin B12 transporter BtuB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,78512
Polymers66,3031
Non-polymers2,48211
Water2,342130
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)81.681, 81.681, 227.148
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein Vitamin B12 transporter BtuB / Cobalamin receptor / Outer membrane cobalamin translocator


Mass: 66303.109 Da / Num. of mol.: 1 / Mutation: W371R1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: btuB, bfe, cer, dcrC, b3966, JW3938 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) pLysS / References: UniProt: P06129
#2: Chemical
ChemComp-C8E / (HYDROXYETHYLOXY)TRI(ETHYLOXY)OCTANE


Mass: 306.438 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C16H34O5 / Comment: C8E, detergent*YM
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-MTN / S-[(1-oxyl-2,2,5,5-tetramethyl-2,5-dihydro-1H-pyrrol-3-yl)methyl] methanesulfonothioate / MTSL / MTSL


Mass: 264.385 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H18NO3S2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 130 / 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: 3.3 Å3/Da / Density % sol: 62.72 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 6.6
Details: 3.0% PEG3350, 200 mM magnesium acetate, 10 mM C8E4, 20 mM Bis Tris pH 6.6, VAPOR DIFFUSION, HANGING DROP, temperature 290K

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Data collection

DiffractionMean temperature: 90 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Oct 14, 2010
RadiationMonochromator: Si 111. Rosenbaum-Rock double-crystal monochromator: liquid nitrogen cooled; sagitally focusing 2nd crystal, Rosenbaum-Rock vertical focusing mirror.
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. all: 37950 / Num. obs: 37950 / % possible obs: 95.2 % / Observed criterion σ(F): 1.5 / Observed criterion σ(I): 2.1 / Redundancy: 7 % / Rmerge(I) obs: 0.105
Reflection shellResolution: 2.3→2.38 Å / % possible all: 76

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Processing

Software
NameVersionClassification
MAR345SERGUIdata collection
PHASERphasing
REFMAC5.5.0102refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→33.38 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.928 / SU B: 11.183 / SU ML: 0.127 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.213 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24981 1911 5 %RANDOM
Rwork0.22004 ---
all0.257 35973 --
obs0.22156 35973 95.18 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 56.254 Å2
Baniso -1Baniso -2Baniso -3
1-0.02 Å20.01 Å20 Å2
2--0.02 Å20 Å2
3----0.02 Å2
Refinement stepCycle: LAST / Resolution: 2.3→33.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4320 0 162 130 4612
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.0214575
X-RAY DIFFRACTIONr_bond_other_d0.0020.023117
X-RAY DIFFRACTIONr_angle_refined_deg1.9531.9546170
X-RAY DIFFRACTIONr_angle_other_deg13.0017520
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0485545
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.36523.839224
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.21315668
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.1281529
X-RAY DIFFRACTIONr_chiral_restr0.1150.2645
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.025070
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02976
X-RAY DIFFRACTIONr_mcbond_it1.1071.52696
X-RAY DIFFRACTIONr_mcbond_other0.2741.51146
X-RAY DIFFRACTIONr_mcangle_it2.07124321
X-RAY DIFFRACTIONr_scbond_it3.16231879
X-RAY DIFFRACTIONr_scangle_it5.0384.51849
LS refinement shellResolution: 2.304→2.363 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.399 123 -
Rwork0.406 2007 -
obs--74.04 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.879-0.28750.09661.87020.31631.8671-0.1292-0.1647-0.16520.24390.10690.13330.2197-0.04940.02230.05760.04140.01530.3821-0.0480.1894-22.672227.081-24.8395
21.412-0.2037-0.1450.91870.12341.096-0.1259-0.2188-0.08980.22310.12120.02860.15830.00980.00470.0770.0538-0.00630.3632-0.07450.1352-22.687229.2537-22.4384
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A6 - 135
2X-RAY DIFFRACTION2A137 - 594

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