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- PDB-1nqh: OUTER MEMBRANE COBALAMIN TRANSPORTER (BTUB) FROM E. COLI, WITH BO... -

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Entry
Database: PDB / ID: 1nqh
TitleOUTER MEMBRANE COBALAMIN TRANSPORTER (BTUB) FROM E. COLI, WITH BOUND CALCIUM AND CYANOCOBALAMIN (VITAMIN B12) SUBSTRATE
ComponentsVITAMIN B12 RECEPTOR
KeywordsTRANSPORT PROTEIN / beta barrel / cobalamin / vitamin B12 / membrane transport / calcium binding
Function / homology
Function and homology information


ABC-type vitamin B12 transporter activity / cobalamin transport / transmembrane transporter complex / porin activity / pore complex / monoatomic ion transmembrane transport / cell outer membrane / 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, beta-barrel domain / TonB-dependent receptor, plug domain / Maltoporin; Chain A / TonB-dependent receptor (TBDR) proteins profile. / TonB box, conserved site / Ferric Hydroxamate Uptake Protein; Chain A, domain 1 / TonB-dependent receptor, conserved site / TonB-dependent receptor (TBDR) proteins signature 2. ...TonB-dependent vitamin B12 transporter BtuB / TonB-dependent receptor (TBDR) proteins signature 1. / TonB-dependent receptor, beta-barrel domain / TonB-dependent receptor, plug domain / Maltoporin; Chain A / TonB-dependent receptor (TBDR) proteins profile. / TonB box, conserved site / Ferric Hydroxamate Uptake Protein; Chain A, domain 1 / TonB-dependent receptor, conserved site / TonB-dependent receptor (TBDR) proteins signature 2. / Vitamin B12 transporter BtuB-like / TonB-dependent receptor-like, beta-barrel / TonB dependent receptor / TonB-dependent receptor, plug domain superfamily / TonB-dependent receptor, plug domain / TonB-dependent receptor-like, beta-barrel domain superfamily / TonB-dependent Receptor Plug Domain / Beta Complex / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
CYANOCOBALAMIN / Vitamin B12 transporter BtuB
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT, SAD / Resolution: 3.1 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 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_struct_conn_angle / 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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_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.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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.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.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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 2.1Aug 16, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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)69,74112
Polymers66,3861
Non-polymers3,35511
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)81.687, 81.687, 225.814
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: pET22b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: P06129
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-CNC / CYANOCOBALAMIN / Cyanocobalamin


Mass: 1356.373 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C63H89CoN14O14P / Comment: medication*YM
#4: Chemical
ChemComp-C8E / (HYDROXYETHYLOXY)TRI(ETHYLOXY)OCTANE


Mass: 306.438 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C16H34O5 / Comment: C8E, detergent*YM

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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: 3.28 Å3/Da / Density % sol: 62.44 %
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: NSLS / Beamline: X25 / Wavelength: 1.6037 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 5, 2002
RadiationMonochromator: Pt-coated toroidal Si mirror for horizontal and vertical focusing followed by double flat Si crystal
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.6037 Å / Relative weight: 1
ReflectionResolution: 3.1→20 Å / Num. all: 30657 / Num. obs: 30643 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 6.3 % / Rsym value: 0.07 / Net I/σ(I): 28.2
Reflection shellResolution: 3.1→3.21 Å / Redundancy: 6.31 % / Mean I/σ(I) obs: 5.2 / Num. unique all: 193476 / Rsym value: 0.115 / % possible all: 99.6
Reflection
*PLUS
Lowest resolution: 20 Å / Num. obs: 16612 / % possible obs: 100 % / Redundancy: 5.8 % / Rmerge(I) obs: 0.073
Reflection shell
*PLUS
Highest resolution: 3.1 Å / % possible obs: 99.7 % / Rmerge(I) obs: 0.35

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Processing

Software
NameVersionClassification
HKL-2000data collection
SCALEPACKdata scaling
AMoREphasing
SHARPphasing
REFMAC5.1.24refinement
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT, SAD
Starting model: PDB ENTRY 1NQF

1nqf


Resolution: 3.1→20 Å / Cor.coef. Fo:Fc: 0.899 / Cor.coef. Fo:Fc free: 0.867 / SU B: 25.129 / SU ML: 0.471 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: TLS / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.464 / 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
Rfree0.2646 837 5.1 %RANDOM
Rwork0.2238 ---
obs0.2259 15679 99.85 %-
all-15703 --
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: 23.448 Å2
Baniso -1Baniso -2Baniso -3
1--0.91 Å2-0.46 Å20 Å2
2---0.91 Å20 Å2
3---1.37 Å2
Refine analyzeLuzzati sigma a free: 0.464 Å
Refinement stepCycle: LAST / Resolution: 3.1→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4630 0 223 0 4853
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0320.0214971
X-RAY DIFFRACTIONr_bond_other_d0.0010.024235
X-RAY DIFFRACTIONr_angle_refined_deg3.0971.9696757
X-RAY DIFFRACTIONr_angle_other_deg1.25939851
X-RAY DIFFRACTIONr_dihedral_angle_1_deg12.1593582
X-RAY DIFFRACTIONr_dihedral_angle_3_deg25.74915735
X-RAY DIFFRACTIONr_chiral_restr0.4090.2703
X-RAY DIFFRACTIONr_gen_planes_refined0.0430.025535
X-RAY DIFFRACTIONr_gen_planes_other0.0180.021061
X-RAY DIFFRACTIONr_nbd_refined0.3910.31778
X-RAY DIFFRACTIONr_nbd_other0.3660.35706
X-RAY DIFFRACTIONr_nbtor_other0.0680.517
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2340.5429
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.236
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2960.327
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3320.396
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2750.53
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_mcbond_it2.2381.52874
X-RAY DIFFRACTIONr_mcangle_it3.63224613
X-RAY DIFFRACTIONr_scbond_it5.94932097
X-RAY DIFFRACTIONr_scangle_it8.6614.52144
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.1→3.175 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.389 57
Rwork0.236 1089
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)
14.0969-0.06391.37381.8696-0.4161.7441-0.00580.1212-0.1386-0.03430.00740.05560.2263-0.1772-0.00170.29090.16660.1140.11070.02610.1446-6.598464.852624.8335
21.05580.03240.23321-0.15471.2592-0.01090.3471-0.1297-0.1492-0.01980.02970.0599-0.06520.03070.26050.16750.07910.19970.04830.2118-5.339766.628820.2801
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: 3.1 Å / Lowest resolution: 20 Å / % reflection Rfree: 5 % / Rfactor Rfree: 0.26 / Rfactor Rwork: 0.224
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.032
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg3.13

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