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

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Basic information

Entry
Database: PDB / ID: 1nqg
TitleOUTER MEMBRANE COBALAMIN TRANSPORTER (BTUB) FROM E. COLI, WITH BOUND CALCIUM
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
Vitamin B12 transporter BtuB
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.31 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 / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

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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)68,38511
Polymers66,3861
Non-polymers1,99910
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)81.632, 81.632, 225.685
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 BTUB


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-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: 3.27 Å3/Da / Density % sol: 62.37 %
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: APS / Beamline: 17-ID / Wavelength: 1.255 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Aug 2, 2002
RadiationMonochromator: Si(111) double-crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.255 Å / Relative weight: 1
ReflectionResolution: 3.3→35 Å / Num. all: 13745 / Num. obs: 13146 / % possible obs: 95.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 9.7 % / Rsym value: 0.079 / Net I/σ(I): 30.4
Reflection shellResolution: 3.3→3.33 Å / Redundancy: 9.4 % / Mean I/σ(I) obs: 8.6 / Num. unique all: 316 / Rsym value: 0.22 / % possible all: 95.8
Reflection
*PLUS
Lowest resolution: 20 Å / Rmerge(I) obs: 0.079
Reflection shell
*PLUS
Highest resolution: 3.3 Å / % possible obs: 95.8 % / Rmerge(I) obs: 0.22

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Processing

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

1nqf


Resolution: 3.31→20 Å / Cor.coef. Fo:Fc: 0.887 / Cor.coef. Fo:Fc free: 0.874 / SU B: 30.727 / SU ML: 0.539 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: TLS / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.546 / 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
Rfree0.259 642 5 %RANDOM
Rwork0.234 ---
all0.236 12961 --
obs0.236 12327 95.11 %-
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: 31.768 Å2
Baniso -1Baniso -2Baniso -3
1--0.55 Å2-0.27 Å20 Å2
2---0.55 Å20 Å2
3---0.82 Å2
Refine analyzeLuzzati sigma a free: 0.539 Å
Refinement stepCycle: LAST / Resolution: 3.31→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4555 0 130 0 4685
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0280.0214786
X-RAY DIFFRACTIONr_bond_other_d0.0010.024141
X-RAY DIFFRACTIONr_angle_refined_deg2.6191.9396466
X-RAY DIFFRACTIONr_angle_other_deg1.05339632
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0943573
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.59215724
X-RAY DIFFRACTIONr_chiral_restr0.1350.2673
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.025359
X-RAY DIFFRACTIONr_gen_planes_other0.0080.021030
X-RAY DIFFRACTIONr_nbd_refined0.3720.31476
X-RAY DIFFRACTIONr_nbd_other0.3540.35156
X-RAY DIFFRACTIONr_nbtor_other0.0580.510
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2260.5379
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.320.5
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2620.318
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3250.393
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2280.52
X-RAY DIFFRACTIONr_mcbond_it4.911.52831
X-RAY DIFFRACTIONr_mcangle_it7.53624542
X-RAY DIFFRACTIONr_scbond_it10.80831955
X-RAY DIFFRACTIONr_scangle_it14.944.51924
LS refinement shellResolution: 3.31→3.389 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.272 51
Rwork0.204 848
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)
13.304-0.0030.25282.19190.1112.80260.00550.232-0.20250.09490.03870.14980.1384-0.2587-0.04410.51190.31610.23260.21460.0840.2902-6.533664.302924.8608
21.92510.022-0.02211.2938-0.06351.4063-0.08450.5501-0.1292-0.16610.05730.11530.1062-0.22630.02720.56390.29550.19830.32080.12760.3455-5.183565.982121.057
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
Software
*PLUS
Version: 5.1.24 / Classification: refinement
Refinement
*PLUS
Highest resolution: 3.3 Å / Lowest resolution: 20 Å / % reflection Rfree: 5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.028
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg2.62

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