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- PDB-1n2z: 2.0 Angstrom structure of BtuF, the vitamin B12 binding protein o... -

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Basic information

Entry
Database: PDB / ID: 1n2z
Title2.0 Angstrom structure of BtuF, the vitamin B12 binding protein of E. coli
ComponentsVitamin B12 transport protein btuF
KeywordsTRANSPORT PROTEIN
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
: / CYANOCOBALAMIN / Vitamin B12-binding protein
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / MAD / Resolution: 2 Å
AuthorsBorths, E.L. / Locher, K.P. / Lee, A.T. / Rees, D.C.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2002
Title: The structure of Escherichia coli BtuF and binding to its cognate ATP binding cassette transporter
Authors: Borths, E.L. / Locher, K.P. / Lee, A.T. / Rees, D.C.
History
DepositionOct 24, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 18, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 2.0Aug 18, 2021Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Non-polymer description / Structure summary
Category: chem_comp / database_2 ...chem_comp / database_2 / entity / pdbx_entity_nonpoly / pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms / pdbx_validate_chiral / struct_conn / struct_site
Item: _chem_comp.formula / _chem_comp.formula_weight ..._chem_comp.formula / _chem_comp.formula_weight / _chem_comp.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.formula_weight / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _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 protein btuF
B: Vitamin B12 transport protein btuF
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,68633
Polymers54,0942
Non-polymers5,59331
Water6,792377
1
A: Vitamin B12 transport protein btuF
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,20120
Polymers27,0471
Non-polymers3,15419
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Vitamin B12 transport protein btuF
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,48613
Polymers27,0471
Non-polymers2,43912
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5410 Å2
ΔGint-160 kcal/mol
Surface area22880 Å2
MethodPISA
4
A: Vitamin B12 transport protein btuF
hetero molecules

B: Vitamin B12 transport protein btuF
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,68633
Polymers54,0942
Non-polymers5,59331
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555y,-x+y,z+1/61
Buried area5320 Å2
ΔGint-161 kcal/mol
Surface area22970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)133.066, 133.066, 67.687
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Vitamin B12 transport protein btuF


Mass: 27046.812 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: btuf / Plasmid: pET22b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 DE3 / References: UniProt: P37028

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Non-polymers , 5 types, 408 molecules

#2: Chemical...
ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 22 / Source method: obtained synthetically / Formula: Cd
#3: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-CNC / CYANOCOBALAMIN / Cyanocobalamin


Mass: 1356.373 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C63H89CoN14O14P / Comment: medication*YM
#5: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL / Polyethylene glycol


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 377 / 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: 3.2 Å3/Da / Density % sol: 61.51 %
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 4.6 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
11 mMVitaminB121drop
215-20 mg/mlprotein1drop
330 %PEG4001reservoir
40.1 Msodium acetate1reservoirpH4.6
50.1 M1reservoirCdCl2

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Data collection

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2→20 Å / Num. obs: 46346 / Observed criterion σ(I): -3
Reflection
*PLUS
Highest resolution: 2 Å / Lowest resolution: 20 Å / % possible obs: 100 % / Redundancy: 10.1 % / Rmerge(I) obs: 0.058
Reflection shell
*PLUS
% possible obs: 100 % / Rmerge(I) obs: 0.182 / Mean I/σ(I) obs: 11.1

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Processing

RefinementMethod to determine structure: MAD / Resolution: 2→20 Å / Cross valid method: THROUGHOUT
RfactorNum. reflectionSelection details
Rfree0.2102 4651 random
Rwork0.189 --
all0.189 41592 -
obs0.189 41592 -
Refinement stepCycle: LAST / Resolution: 2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3816 0 223 377 4416
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.0067
X-RAY DIFFRACTIONc_angle_deg1.32
Refinement
*PLUS
Lowest resolution: 20 Å / Rfactor Rfree: 0.21
Solvent computation
*PLUS
Displacement parameters
*PLUS

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