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- PDB-5m2q: Structure of cobinamide-bound BtuF mutant W66F, the periplasmic v... -

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Basic information

Entry
Database: PDB / ID: 5m2q
TitleStructure of cobinamide-bound BtuF mutant W66F, the periplasmic vitamin B12 binding protein in E.coli
ComponentsOuter membrane protein A,Vitamin B12-binding protein
KeywordsTRANSPORT PROTEIN / BtuF / Cobinamide / periplasmic binding protein / ABC transporter
Function / homology
Function and homology information


cobalamin transport complex / outer membrane protein complex / cobalamin transport / monoatomic ion transmembrane transporter activity / detection of virus / outer membrane / cobalamin binding / porin activity / pore complex / monoatomic ion transport ...cobalamin transport complex / outer membrane protein complex / cobalamin transport / monoatomic ion transmembrane transporter activity / detection of virus / outer membrane / cobalamin binding / porin activity / pore complex / monoatomic ion transport / cell outer membrane / outer membrane-bounded periplasmic space / periplasmic space / DNA damage response / symbiont entry into host cell / identical protein binding / membrane
Similarity search - Function
ABC transporter, vitamin B12-binding protein / : / Outer membrane protein OmpA-like, transmembrane domain / Outer membrane protein, OmpA / OmpA-like transmembrane domain / : / Outer membrane protein, OmpA-like, conserved site / OmpA-like domain. / Outer membrane protein, bacterial / ABC transporter periplasmic binding domain ...ABC transporter, vitamin B12-binding protein / : / Outer membrane protein OmpA-like, transmembrane domain / Outer membrane protein, OmpA / OmpA-like transmembrane domain / : / Outer membrane protein, OmpA-like, conserved site / OmpA-like domain. / Outer membrane protein, bacterial / ABC transporter periplasmic binding domain / Periplasmic binding protein / Iron siderophore/cobalamin periplasmic-binding domain profile. / : / OmpA-like domain profile. / OmpA-like domain superfamily / OmpA family / OmpA-like domain / Nitrogenase molybdenum iron protein domain / Outer membrane protein/outer membrane enzyme PagP, beta-barrel / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
COB(II)INAMIDE / CYANIDE ION / Outer membrane protein A / Vitamin B12-binding protein
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 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 13, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 1, 2017Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2019Group: Data collection / Category: reflns_shell
Revision 1.2Jan 17, 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 1.3Oct 23, 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: Outer membrane protein A,Vitamin B12-binding protein
B: Outer membrane protein A,Vitamin B12-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,2549
Polymers62,9462
Non-polymers2,3087
Water7,026390
1
A: Outer membrane protein A,Vitamin B12-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,6735
Polymers31,4731
Non-polymers1,2004
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Outer membrane protein A,Vitamin B12-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,5814
Polymers31,4731
Non-polymers1,1083
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)136.560, 90.670, 50.810
Angle α, β, γ (deg.)90.00, 110.87, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Outer membrane protein A,Vitamin B12-binding protein / Outer membrane protein II*


Mass: 31472.889 Da / Num. of mol.: 2 / Mutation: W66F
Source method: isolated from a genetically manipulated source
Details: OmpA-NcoI-BtuF-BamHI-3C-BamHI-His6 / Source: (gene. exp.) Escherichia coli (E. coli)
Gene: ompA, con, tolG, tut, b0957, JW0940, btuF, yadT, b0158, JW0154
Production host: Escherichia coli (E. coli) / References: UniProt: P0A910, UniProt: P37028
#2: Chemical ChemComp-CBY / COB(II)INAMIDE


Mass: 990.087 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C48H72CoN11O8
#3: Chemical ChemComp-CYN / CYANIDE ION


Mass: 26.017 Da / Num. of mol.: 2 / 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: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 390 / 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: 2.33 Å3/Da / Density % sol: 47.32 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / Details: PEG3350 HEPES pH 7 Tryptone

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Data collection

DiffractionMean temperature: 123 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.97794 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Dec 13, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97794 Å / Relative weight: 1
ReflectionResolution: 1.7→19.71 Å / Num. obs: 61170 / % possible obs: 96.27 % / Redundancy: 3.1 % / Net I/σ(I): 11.05

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Processing

Software
NameVersionClassification
REFMAC5.8.0071refinement
PHENIX1.10.1-2155refinement
XSCALEdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5M29

5m29


Resolution: 1.7→19.71 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.944 / SU B: 8.866 / SU ML: 0.132 / Cross valid method: THROUGHOUT / ESU R: 0.114 / ESU R Free: 0.116 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24923 3060 5 %RANDOM
Rwork0.20886 ---
obs0.21087 58109 96.27 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 33.948 Å2
Baniso -1Baniso -2Baniso -3
1--0.24 Å20 Å2-0.34 Å2
2--0.07 Å20 Å2
3---0.34 Å2
Refinement stepCycle: 1 / Resolution: 1.7→19.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3532 0 158 390 4080
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.023784
X-RAY DIFFRACTIONr_bond_other_d0.0010.023694
X-RAY DIFFRACTIONr_angle_refined_deg2.3082.0175193
X-RAY DIFFRACTIONr_angle_other_deg0.89838478
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5935454
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.74625.19158
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.08115608
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.861522
X-RAY DIFFRACTIONr_chiral_restr0.1940.2593
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0214281
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02851
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_it1.7451.5891824
X-RAY DIFFRACTIONr_mcbond_other1.7391.5881822
X-RAY DIFFRACTIONr_mcangle_it2.8492.3652271
X-RAY DIFFRACTIONr_mcangle_other2.8492.3672272
X-RAY DIFFRACTIONr_scbond_it2.311.831960
X-RAY DIFFRACTIONr_scbond_other2.311.831960
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.5322.622922
X-RAY DIFFRACTIONr_long_range_B_refined8.5514.7364716
X-RAY DIFFRACTIONr_long_range_B_other8.54914.7364716
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.482 227 -
Rwork0.504 4309 -
obs--97.36 %
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)
10.5620.33920.04850.8169-0.05280.21610.1526-0.0822-0.0278-0.0928-0.09420.05780.00180.0215-0.05830.3525-0.00630.05750.05670.00590.0489-46.855-26.9064-15.6164
20.616-0.4125-0.26810.60240.04350.1886-0.12790.0460.03570.17590.0893-0.08630.1053-0.07340.03860.5183-0.00670.10780.0463-0.02740.0515-33.6211-20.34985.7516
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A23 - 266
2X-RAY DIFFRACTION2B21 - 265

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