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- PDB-1l7v: Bacterial ABC Transporter Involved in B12 Uptake -

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Basic information

Entry
Database: PDB / ID: 1l7v
TitleBacterial ABC Transporter Involved in B12 Uptake
Components
  • VITAMIN B12 TRANSPORT SYSTEM PERMEASE PROTEIN BTUC
  • Vitamin B12 transport ATP-binding protein btuD
KeywordsTRANSPORT PROTEIN/HYDROLASE / ABC transporter / integral membrane protein / ATP binding cassette / ATP hydrolysis / Vitamin B12 / TRANSPORT PROTEIN-HYDROLASE COMPLEX
Function / homology
Function and homology information


BtuCD complex / ABC-type vitamin B12 transporter / cobalamin transport complex / ABC-type vitamin B12 transporter activity / cobalamin transport / extrinsic component of membrane / transmembrane transporter activity / ATPase-coupled transmembrane transporter activity / ATP-binding cassette (ABC) transporter complex / ATP hydrolysis activity ...BtuCD complex / ABC-type vitamin B12 transporter / cobalamin transport complex / ABC-type vitamin B12 transporter activity / cobalamin transport / extrinsic component of membrane / transmembrane transporter activity / ATPase-coupled transmembrane transporter activity / ATP-binding cassette (ABC) transporter complex / ATP hydrolysis activity / ATP binding / identical protein binding / membrane / plasma membrane
Similarity search - Function
ABC transporter, vitamin B12 import, permease protein BtuC / ABC transporter, vitamin B12, BtuD / : / ABC transporter, permease protein, BtuC-like / FecCD transport family / ABC transporter involved in vitamin B12 uptake, BtuC / ABC transporter involved in vitamin B12 uptake, BtuC / ABC transporter, BtuC-like / ABC transporter-like, conserved site / ABC transporters family signature. ...ABC transporter, vitamin B12 import, permease protein BtuC / ABC transporter, vitamin B12, BtuD / : / ABC transporter, permease protein, BtuC-like / FecCD transport family / ABC transporter involved in vitamin B12 uptake, BtuC / ABC transporter involved in vitamin B12 uptake, BtuC / ABC transporter, BtuC-like / 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 / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
CYCLO-TETRAMETAVANADATE / Vitamin B12 import system permease protein BtuC / Vitamin B12 import ATP-binding protein BtuD
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 3.2 Å
AuthorsLocher, K.P. / Lee, A.T. / Rees, D.C.
CitationJournal: Science / Year: 2002
Title: The E. coli BtuCD structure: a framework for ABC transporter architecture and mechanism.
Authors: Locher, K.P. / Lee, A.T. / Rees, D.C.
History
DepositionMar 18, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 15, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 20, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / 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 TRANSPORT SYSTEM PERMEASE PROTEIN BTUC
B: VITAMIN B12 TRANSPORT SYSTEM PERMEASE PROTEIN BTUC
C: Vitamin B12 transport ATP-binding protein btuD
D: Vitamin B12 transport ATP-binding protein btuD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)126,8406
Polymers126,0484
Non-polymers7922
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8920 Å2
ΔGint-84 kcal/mol
Surface area45790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.990, 106.292, 95.543
Angle α, β, γ (deg.)90.00, 99.29, 90.00
Int Tables number4
Space group name H-MP1211
DetailsAsymmetric unit contains full transporter: two copies each of BtuC and BtuD

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Components

#1: Protein VITAMIN B12 TRANSPORT SYSTEM PERMEASE PROTEIN BTUC


Mass: 35487.941 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: BTUC / Production host: Escherichia coli (E. coli) / References: UniProt: P06609
#2: Protein Vitamin B12 transport ATP-binding protein btuD / Vitamin B12-transporting ATPase


Mass: 27536.234 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: BTUD / Production host: Escherichia coli (E. coli) / References: UniProt: P06611, EC: 3.6.3.33
#3: Chemical ChemComp-V4O / CYCLO-TETRAMETAVANADATE


Mass: 395.759 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: O12V4
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: 3.7 Å3/Da / Density % sol: 66.72 %
Crystal growTemperature: 278 K / Method: vapor diffusion, sitting drop / pH: 8
Details: PEG 2000, LDAO, Tris, magnesium nitrate, MPD, D2O, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 278K
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
120 mg/mlprotein1drop
2100 mMTris1reservoirpH8.0
3300 mMmagnesium nitrate1reservoir
421 %PEG20001reservoir
50.8 %MPD1reservoirin D2O

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 1.7712 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Dec 18, 2001
RadiationMonochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.7712 Å / Relative weight: 1
ReflectionResolution: 3.2→30 Å / Num. all: 30814 / Num. obs: 30660 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3
Reflection shellResolution: 3.2→3.29 Å / % possible all: 94.3
Reflection
*PLUS
Lowest resolution: 30 Å / Redundancy: 8.2 % / Rmerge(I) obs: 0.067
Reflection shell
*PLUS
% possible obs: 94.3 % / Rmerge(I) obs: 0.448 / Mean I/σ(I) obs: 4.1

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Processing

Software
NameVersionClassification
SHARPphasing
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MAD / Resolution: 3.2→15 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.286 2944 Random
Rwork0.262 --
all-30126 -
obs-30066 -
Refinement stepCycle: LAST / Resolution: 3.2→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8378 0 32 0 8410
Refinement
*PLUS
Lowest resolution: 15 Å / Rfactor obs: 0.262 / Rfactor Rfree: 0.286 / Rfactor Rwork: 0.262
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONo_bond_d0.005
X-RAY DIFFRACTIONo_angle_d
X-RAY DIFFRACTIONo_angle_deg1.12

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