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- PDB-1nqe: OUTER MEMBRANE COBALAMIN TRANSPORTER (BTUB) FROM E. COLI -

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Basic information

Entry
Database: PDB / ID: 1nqe
TitleOUTER MEMBRANE COBALAMIN TRANSPORTER (BTUB) FROM E. COLI
ComponentsVitamin B12 receptor
KeywordsTRANSPORT PROTEIN / BETA BARREL / cobalamin / VITAMIN B12 / OUTER MEMBRANE TRANSPORT
Function / homology
Function and homology information


ABC-type vitamin B12 transporter activity / cobalamin transport / transmembrane transporter complex / porin activity / pore complex / cell outer membrane / monoatomic ion transmembrane transport / protein domain specific binding / calcium ion binding / membrane
Similarity search - Function
TonB-dependent vitamin B12 transporter BtuB / TonB-dependent receptor (TBDR) proteins signature 1. / TonB-dependent receptor, plug domain / TonB box, conserved site / Ferric Hydroxamate Uptake Protein; Chain A, domain 1 / TonB-dependent receptor, beta-barrel domain / TonB-dependent receptor, conserved site / TonB-dependent receptor (TBDR) proteins signature 2. / Maltoporin; Chain A / TonB-dependent receptor-like, beta-barrel ...TonB-dependent vitamin B12 transporter BtuB / TonB-dependent receptor (TBDR) proteins signature 1. / TonB-dependent receptor, plug domain / TonB box, conserved site / Ferric Hydroxamate Uptake Protein; Chain A, domain 1 / TonB-dependent receptor, beta-barrel domain / TonB-dependent receptor, conserved site / TonB-dependent receptor (TBDR) proteins signature 2. / Maltoporin; Chain A / TonB-dependent receptor-like, beta-barrel / TonB dependent receptor-like, beta-barrel / TonB-dependent receptor (TBDR) proteins profile. / Vitamin B12 transporter BtuB-like / TonB-dependent receptor, plug domain superfamily / TonB-dependent receptor, plug domain / TonB-dependent Receptor Plug Domain / TonB-dependent receptor-like, beta-barrel domain superfamily / Beta Complex / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Vitamin B12 transporter BtuB
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsChimento, D.P. / Mohanty, A.K. / Kadner, R.J. / Wiener, M.C.
Citation
Journal: Nat.Struct.Biol. / Year: 2003
Title: Substrate-induced transmembrane signaling in the cobalamin transporter BtuB
Authors: Chimento, D.P. / Mohanty, A.K. / Kadner, R.J. / Wiener, M.C.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 2003
Title: Crystallization and initial X-ray diffraction of BtuB, the integral membrane cobalamin transporter of Escherichia coli
Authors: Chimento, D.P. / Mohanty, A.K. / Kadner, R.J. / Wiener, M.C.
History
DepositionJan 21, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 29, 2003Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Aug 16, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_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_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_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 receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,5569
Polymers66,3861
Non-polymers2,1698
Water4,234235
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)81.590, 81.590, 210.078
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein Vitamin B12 receptor / OUTER MEMBRANE COBALAMIN TRANSPORTER


Mass: 66386.180 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: btuB / Plasmid: pET21b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)plysS / References: UniProt: P06129
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Chemical
ChemComp-C8E / (HYDROXYETHYLOXY)TRI(ETHYLOXY)OCTANE


Mass: 306.438 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C16H34O5 / Comment: C8E, detergent*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 235 / 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: 3.04 Å3/Da / Density % sol: 59.54 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.6
Details: PEG 3350, magnesium acetate, bis-tris, n-octyl tetraoxyethylene , pH 6.6, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal grow
*PLUS
Details: Chimento, D.P., (2003) Acta Crystallogr., Sect.D, 59, 509.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
112 mg/mlprotein1drop
2200-400 mMmagnesium acetate1reservoir
34-7 %PEG33501reservoir
450 mMcacodylate1reservoirpH6.6
520 mM1reservoirC8E4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.9 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Aug 26, 2000 / Details: Rh-coated Si mirror
RadiationMonochromator: Bent triangular asymmetric cut Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2→25 Å / Num. all: 56085 / Num. obs: 55698 / % possible obs: 99.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 8.4 % / Rsym value: 0.065 / Net I/σ(I): 31.5
Reflection shellResolution: 2→2.07 Å / Redundancy: 5.9 % / Mean I/σ(I) obs: 1.69 / Num. unique all: 5362 / Rsym value: 0.412 / % possible all: 97.8
Reflection
*PLUS
Lowest resolution: 25 Å / Num. obs: 55620 / % possible obs: 99.6 % / Redundancy: 8.9 % / Rmerge(I) obs: 0.065
Reflection shell
*PLUS
Highest resolution: 2 Å / Lowest resolution: 2.18 Å / % possible obs: 97.8 % / Rmerge(I) obs: 0.412

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1NQF

1nqf


Resolution: 2→24.92 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.945 / SU B: 3.83 / SU ML: 0.105 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: TLS / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.149 / ESU R Free: 0.142 / Stereochemistry target values: Engh & Huber
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. THE AVERAGE ISOTROPIC B VALUE IS AN AVERAGE RESIDUAL B FACTOR.
RfactorNum. reflection% reflectionSelection details
Rfree0.23154 2793 5 %RANDOM
Rwork0.1943 ---
all0.19618 56085 --
obs0.19618 52523 99.32 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 41.151 Å2
Baniso -1Baniso -2Baniso -3
1-1.51 Å20.76 Å20 Å2
2--1.51 Å20 Å2
3----2.27 Å2
Refine analyzeLuzzati sigma a free: 0.142 Å
Refinement stepCycle: LAST / Resolution: 2→24.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4350 0 148 235 4733
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0214595
X-RAY DIFFRACTIONr_bond_other_d0.0840.024027
X-RAY DIFFRACTIONr_angle_refined_deg1.6261.9456192
X-RAY DIFFRACTIONr_angle_other_deg1.21139366
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2065545
X-RAY DIFFRACTIONr_chiral_restr0.1130.2643
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.025092
X-RAY DIFFRACTIONr_gen_planes_other0.0310.02989
X-RAY DIFFRACTIONr_nbd_refined0.2460.2767
X-RAY DIFFRACTIONr_nbd_other0.3280.24820
X-RAY DIFFRACTIONr_nbtor_other0.0990.22815
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1660.2212
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.5060.219
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3980.2114
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1460.24
X-RAY DIFFRACTIONr_mcbond_it6.4341.52696
X-RAY DIFFRACTIONr_mcangle_it8.67524324
X-RAY DIFFRACTIONr_scbond_it14.00631899
X-RAY DIFFRACTIONr_scangle_it16.6294.51868
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.324 190
Rwork0.257 3603
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)
10.96220.17010.15810.5906-0.00870.5616-0.01320.0348-0.0466-0.02010.00560.05950.0754-0.09580.00760.10780.07880.00560.0587-0.00550.0899-5.241661.707122.3128
20.3303-0.01810.05170.33610.06280.258-0.01810.0631-0.0065-0.02420.00850.02320.0291-0.0510.00960.11230.05030.01860.08590.00590.1033-3.579162.967519.9068
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA6 - 1366 - 136
2X-RAY DIFFRACTION2AA137 - 594137 - 594
Refinement
*PLUS
Highest resolution: 2 Å / Lowest resolution: 25 Å / % reflection Rfree: 5 % / Rfactor Rfree: 0.232 / Rfactor Rwork: 0.194
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.021
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg1.95

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