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- PDB-1n4a: The Ligand Bound Structure of E.coli BtuF, the Periplasmic Bindin... -

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Basic information

Entry
Database: PDB / ID: 1n4a
TitleThe Ligand Bound Structure of E.coli BtuF, the Periplasmic Binding Protein for Vitamin B12
ComponentsVitamin B12 transport protein btuF
KeywordsTRANSPORT PROTEIN / ABC transporter / periplasmic binding protein / Vitamin B12 / transmembrane transport / Structural Genomics / PSI / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG
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 / SYNCHROTRON / MAD / Resolution: 2 Å
AuthorsKarpowich, N.K. / Smith, P.C. / Hunt, J.F. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: J.Biol.Chem. / Year: 2003
Title: Crystal structures of the BtuF periplasmic-binding protein for vitamin B12 suggest a functionally important reduction in protein mobility upon ligand binding.
Authors: Karpowich, N.K. / Huang, H.H. / Smith, P.C. / Hunt, J.F.
History
DepositionOct 30, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 11, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 8, 2017Group: Database references / Structure summary
Revision 2.0Aug 18, 2021Group: Data collection / Database references ...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_validate_chiral / struct_conn / struct_ref_seq_dif / 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 / _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
Revision 2.1Oct 30, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / 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 transport protein btuF
B: Vitamin B12 transport protein btuF
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,9944
Polymers56,2812
Non-polymers2,7132
Water9,890549
1
A: Vitamin B12 transport protein btuF
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,4972
Polymers28,1411
Non-polymers1,3561
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)29,4972
Polymers28,1411
Non-polymers1,3561
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)131.730, 92.020, 44.690
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Vitamin B12 transport protein btuF


Mass: 28140.680 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Plasmid: pet24A / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(de3) / References: UniProt: P37028
#2: Chemical ChemComp-CNC / CYANOCOBALAMIN


Mass: 1356.373 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C63H89CoN14O14P
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 549 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.13 Å3/Da / Density % sol: 41.81 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: NaCl, ethanol, acetate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 294K
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
15 mMprotein1drop
22.0 M1reservoirNaCl
33 %ethanol1reservoir
4100 mMsodium acetate1reservoirpH4.6

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X12C / Wavelength: 0.9785
DetectorDate: Nov 15, 2002
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9785 Å / Relative weight: 1
ReflectionResolution: 2→20 Å / Num. obs: 34910 / Biso Wilson estimate: 24.8 Å2
Reflection
*PLUS
Highest resolution: 2 Å / Lowest resolution: 20 Å / % possible obs: 98.7 % / Redundancy: 4.5 % / Rmerge(I) obs: 0.056
Reflection shell
*PLUS
% possible obs: 91.9 %

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
CNSrefinement
RefinementMethod to determine structure: MAD / Resolution: 2→20 Å / Rfactor Rfree error: 0.013 / Data cutoff high absF: 1000000 / Data cutoff low absF: 0.01 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.261 1732 5 %RANDOM
Rwork0.234 ---
all-36765 --
obs-34564 24.4 %-
Displacement parametersBiso mean: 31.5 Å2
Baniso -1Baniso -2Baniso -3
1-8.82 Å20 Å20 Å2
2---5.91 Å20 Å2
3----2.91 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.63 Å0.64 Å
Luzzati d res low-2.5 Å
Luzzati sigma a-0.26 Å
Refinement stepCycle: LAST / Resolution: 2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3804 0 186 549 4539
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.006
X-RAY DIFFRACTIONx_angle_deg1.3
X-RAY DIFFRACTIONx_dihedral_angle_d22.5
X-RAY DIFFRACTIONx_improper_angle_d1.31
LS refinement shellResolution: 2→2.09 Å / Rfactor Rfree error: 0.043 / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.262 152 4.7 %
Rwork0.212 3081 -
obs--18.2 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PS_PARAMPS_TOP
X-RAY DIFFRACTION2PARAM1
X-RAY DIFFRACTION3CC
Refinement
*PLUS
Highest resolution: 2 Å / Lowest resolution: 20 Å / Rfactor Rfree: 0.262 / Rfactor Rwork: 0.214
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg22.5
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.31

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