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- PDB-5m29: Structure of cobinamide-bound BtuF, the periplasmic vitamin B12 b... -

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Basic information

Entry
Database: PDB / ID: 5m29
TitleStructure of cobinamide-bound BtuF, the periplasmic vitamin B12 binding protein in E.coli
ComponentsVitamin B12-binding protein
KeywordsTRANSPORT PROTEIN / BtuF / Cobinamide / periplasmic binding protein / ABC transporter
Function / homology
Function and homology information


cobalamin transport complex / cobalamin transport / cobalamin binding / outer membrane-bounded periplasmic space / periplasmic space / membrane
Similarity search - Function
ABC transporter, vitamin B12-binding protein / : / : / ABC transporter periplasmic binding domain / Periplasmic binding protein / Iron siderophore/cobalamin periplasmic-binding domain profile. / Nitrogenase molybdenum iron protein domain / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
COB(II)INAMIDE / CYANIDE ION / Vitamin B12-binding protein
Similarity search - Component
Biological speciesEscherichia coli K-12 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsMireku, S.A. / Ruetz, M. / Zhou, T. / Korkhov, V.M. / Kraeutler, B. / Locher, K.P.
CitationJournal: Sci Rep / Year: 2017
Title: Conformational Change of a Tryptophan Residue in BtuF Facilitates Binding and Transport of Cobinamide by the Vitamin B12 Transporter BtuCD-F.
Authors: Mireku, S.A. / Ruetz, M. / Zhou, T. / Korkhov, V.M. / Krautler, B. / Locher, K.P.
History
DepositionOct 12, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 8, 2017Provider: repository / Type: Initial release
Revision 1.1Apr 25, 2018Group: Data collection / Source and taxonomy / Category: entity_src_gen / reflns / reflns_shell
Item: _entity_src_gen.gene_src_strain / _entity_src_gen.pdbx_gene_src_scientific_name ..._entity_src_gen.gene_src_strain / _entity_src_gen.pdbx_gene_src_scientific_name / _reflns.pdbx_Rmerge_I_obs / _reflns_shell.Rmerge_I_obs
Revision 1.2Feb 7, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Vitamin B12-binding protein
B: Vitamin B12-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,00310
Polymers63,6692
Non-polymers2,3358
Water9,584532
1
A: Vitamin B12-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,0355
Polymers31,8341
Non-polymers1,2004
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Vitamin B12-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,9685
Polymers31,8341
Non-polymers1,1344
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)138.150, 90.560, 50.840
Angle α, β, γ (deg.)90.00, 110.90, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Vitamin B12-binding protein


Mass: 31834.275 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: OmpA-NcoI-BtuF-BamHI-3Csite-BamHI-His6Tag / Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Gene: btuF, yadT, b0158, JW0154 / Production host: Escherichia coli (E. coli) / References: UniProt: P37028
#2: Chemical ChemComp-CBY / COB(II)INAMIDE


Mass: 990.087 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C48H72CoN11O8
#3: Chemical ChemComp-CYN / CYANIDE ION


Mass: 26.017 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: CN
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 532 / 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: 2.61 Å3/Da / Density % sol: 52.81 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / Details: HEPES sodium pH 7.0 PEG3350 Tryptone

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Data collection

DiffractionMean temperature: 123 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1.00001 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Sep 27, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00001 Å / Relative weight: 1
ReflectionResolution: 1.5→29.39 Å / Num. obs: 89615 / % possible obs: 96.02 % / Redundancy: 3.5 % / Rmerge(I) obs: 0.059 / Net I/σ(I): 10.16
Reflection shellResolution: 1.5→1.69 Å / Rmerge(I) obs: 0.849 / Num. measured obs: 8600

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Processing

Software
NameVersionClassification
REFMAC5.8.0071refinement
PHENIX1.8.2-1309refinement
XSCALEdata scaling
XDSdata reduction
PHENIX1.8.2-1309phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1N2Z

1n2z


Resolution: 1.5→29.39 Å / Cor.coef. Fo:Fc: 0.976 / Cor.coef. Fo:Fc free: 0.965 / SU B: 2.661 / SU ML: 0.085 / Cross valid method: THROUGHOUT / ESU R: 0.069 / ESU R Free: 0.074 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21296 4481 5 %RANDOM
Rwork0.17903 ---
obs0.18073 85134 96.02 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 31.424 Å2
Baniso -1Baniso -2Baniso -3
1-3.48 Å20 Å20.49 Å2
2---1.93 Å20 Å2
3----1.49 Å2
Refinement stepCycle: 1 / Resolution: 1.5→29.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3548 0 160 532 4240
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.023836
X-RAY DIFFRACTIONr_bond_other_d0.0010.023731
X-RAY DIFFRACTIONr_angle_refined_deg2.2282.0135272
X-RAY DIFFRACTIONr_angle_other_deg0.90938566
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.765464
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.37225.215163
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.87915615
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.2241523
X-RAY DIFFRACTIONr_chiral_restr0.2240.2598
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0214365
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02868
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.9272.7931844
X-RAY DIFFRACTIONr_mcbond_other2.9212.7911841
X-RAY DIFFRACTIONr_mcangle_it4.2864.1632298
X-RAY DIFFRACTIONr_mcangle_other4.2864.1672299
X-RAY DIFFRACTIONr_scbond_it3.8673.1821992
X-RAY DIFFRACTIONr_scbond_other3.8673.1821992
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.9334.5892971
X-RAY DIFFRACTIONr_long_range_B_refined8.90424.8914819
X-RAY DIFFRACTIONr_long_range_B_other8.90824.8974820
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.5→1.539 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.541 315 -
Rwork0.578 5996 -
obs--91.62 %

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