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- PDB-2qi9: ABC-transporter BtuCD in complex with its periplasmic binding pro... -

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Basic information

Entry
Database: PDB / ID: 2qi9
TitleABC-transporter BtuCD in complex with its periplasmic binding protein BtuF
Components
  • (Vitamin B12 import ...) x 2
  • Vitamin B12-binding protein btuF
KeywordsMEMBRANE PROTEIN / Inner membrane / Membrane / Transmembrane / Transport / ATP-binding / Hydrolase / Nucleotide-binding / Periplasm
Function / homology
Function and homology information


ABC-type vitamin B12 transporter / BtuCD complex / cobalamin transport complex / ABC-type vitamin B12 transporter activity / cobalamin transport / cobalamin binding / extrinsic component of membrane / transmembrane transporter activity / ATPase-coupled transmembrane transporter activity / ATP-binding cassette (ABC) transporter complex ...ABC-type vitamin B12 transporter / BtuCD complex / cobalamin transport complex / ABC-type vitamin B12 transporter activity / cobalamin transport / cobalamin binding / extrinsic component of membrane / transmembrane transporter activity / ATPase-coupled transmembrane transporter activity / ATP-binding cassette (ABC) transporter complex / outer membrane-bounded periplasmic space / periplasmic space / ATP hydrolysis activity / ATP binding / membrane / identical protein binding / plasma membrane
Similarity search - Function
ABC transporter, vitamin B12 import, permease protein BtuC / ABC transporter, vitamin B12, BtuD / ABC transporter involved in vitamin B12 uptake, BtuC / ABC transporter involved in vitamin B12 uptake, BtuC / ABC transporter, permease protein, BtuC-like / FecCD transport family / ABC transporter, vitamin B12-binding protein / ABC transporter, BtuC-like / ABC transporter periplasmic binding domain / Periplasmic binding protein ...ABC transporter, vitamin B12 import, permease protein BtuC / ABC transporter, vitamin B12, BtuD / ABC transporter involved in vitamin B12 uptake, BtuC / ABC transporter involved in vitamin B12 uptake, BtuC / ABC transporter, permease protein, BtuC-like / FecCD transport family / ABC transporter, vitamin B12-binding protein / ABC transporter, BtuC-like / ABC transporter periplasmic binding domain / Periplasmic binding protein / Iron siderophore/cobalamin periplasmic-binding domain profile. / Nitrogenase molybdenum iron protein domain / ABC transporter-like, conserved site / ABC transporters family signature. / ABC transporter / ABC transporter-like, ATP-binding domain / ATP-binding cassette, ABC transporter-type domain profile. / P-loop containing nucleotide triphosphate hydrolases / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / PHOSPHATE ION / Vitamin B12 import system permease protein BtuC / Vitamin B12 import ATP-binding protein BtuD / Vitamin B12-binding protein
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.6 Å
AuthorsHvorup, R.N. / Goetz, B.A. / Niederer, M. / Hollenstein, K. / Perozo, E. / Locher, K.P.
CitationJournal: Science / Year: 2007
Title: Asymmetry in the structure of the ABC transporter-binding protein complex BtuCD-BtuF.
Authors: Hvorup, R.N. / Goetz, B.A. / Niederer, M. / Hollenstein, K. / Perozo, E. / Locher, K.P.
History
DepositionJul 3, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 14, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 18, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Oct 20, 2021Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / struct_conn / 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_conn.pdbx_leaving_atom_flag / _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: Vitamin B12 import system permease protein btuC
B: Vitamin B12 import system permease protein btuC
C: Vitamin B12 import ATP-binding protein btuD
D: Vitamin B12 import ATP-binding protein btuD
F: Vitamin B12-binding protein btuF
hetero molecules


Theoretical massNumber of molelcules
Total (without water)154,59919
Polymers152,9325
Non-polymers1,66714
Water28816
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area19040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)213.582, 127.396, 97.547
Angle α, β, γ (deg.)90.000, 112.760, 90.000
Int Tables number5
Space group name H-MC121

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Components

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Vitamin B12 import ... , 2 types, 4 molecules ABCD

#1: Protein Vitamin B12 import system permease protein btuC


Mass: 35375.488 Da / Num. of mol.: 2 / Mutation: C18S, C32S, C120S, C156S, C205S, C206S, C267S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: btuC / Plasmid: pET19b / Production host: Escherichia coli (E. coli) / References: UniProt: P06609
#2: Protein Vitamin B12 import ATP-binding protein btuD / Vitamin B12-transporting ATPase


Mass: 27520.170 Da / Num. of mol.: 2 / Mutation: C180S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: btuD / Plasmid: pET19b / Production host: Escherichia coli (E. coli) / References: UniProt: P06611, EC: 3.6.3.33

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Protein , 1 types, 1 molecules F

#3: Protein Vitamin B12-binding protein btuF


Mass: 27140.604 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: btuF / Plasmid: pET19b / Production host: Escherichia coli (E. coli) / References: UniProt: P37028

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Non-polymers , 5 types, 30 molecules

#4: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#5: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#6: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400 / Polyethylene glycol


Mass: 238.278 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#7: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H10O3
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 16 / 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: 4 Å3/Da / Density % sol: 69.26 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.4
Details: 30-38% (w/v) polyethylene glycol 400, 50mM either of Tris‑HCl pH 8.4 or Glycine-NaOH pH 9.4 and 400mM (NH4)2SO4., VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.93209, 0.97934, 0.97980
DetectorDate: Feb 18, 2007
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.932091
20.979341
30.97981
ReflectionResolution: 2.586→29.814 Å / Num. all: 74391 / Num. obs: 74100 / % possible obs: 100 % / Redundancy: 4.7 % / Rmerge(I) obs: 0.074 / Rsym value: 0.074
Reflection shellResolution: 2.6→2.69 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.57 / Rsym value: 0.57 / % possible all: 100

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Processing

Software
NameVersionClassificationNB
REFMACrefinement
PDB_EXTRACT3data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
SHARPphasing
CCP4phasing
CNSrefinement
RefinementMethod to determine structure: MAD / Resolution: 2.6→29.814 Å / σ(F): 0
RfactorNum. reflection% reflection
Rfree0.28 3727 5 %
Rwork0.262 --
obs-73847 99.8 %
Solvent computationBsol: 48.132 Å2
Displacement parametersBiso mean: 84.616 Å2
Baniso -1Baniso -2Baniso -3
1-1.434 Å20 Å2-2.662 Å2
2--2.347 Å20 Å2
3----3.78 Å2
Refinement stepCycle: LAST / Resolution: 2.6→29.814 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10576 0 72 44 10692
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1CNS_TOPPAR:protein_rep.param
X-RAY DIFFRACTION2po4.param
X-RAY DIFFRACTION3so4.param
X-RAY DIFFRACTION4pegdeg.param
X-RAY DIFFRACTION5hoh.param

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