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- PDB-1nqf: OUTER MEMBRANE COBALAMIN TRANSPORTER (BTUB) FROM E. COLI, METHION... -

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Basic information

Entry
Database: PDB / ID: 1nqf
TitleOUTER MEMBRANE COBALAMIN TRANSPORTER (BTUB) FROM E. COLI, METHIONINE SUBSTIUTION CONSTRUCT FOR SE-MET SAD PHASING
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 / 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 / SAD/direct method / Resolution: 2.7 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 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software
Revision 1.4Jul 24, 2019Group: Data collection / Derived calculations / Refinement description
Category: software / struct_conn
Item: _software.classification / _software.name ..._software.classification / _software.name / _software.version / _struct_conn.pdbx_leaving_atom_flag
Revision 1.5Oct 27, 2021Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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_ref_seq_dif.details / _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)68,5328
Polymers66,6701
Non-polymers1,8637
Water1,24369
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)81.614, 81.614, 226.653
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: 66669.500 Da / Num. of mol.: 1 / Mutation: W317M, K319M, T321M, W516M, I518M, Y520M
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): B834(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.: 6 / Source method: obtained synthetically / Formula: C16H34O5 / Comment: C8E, detergent*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 69 / 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: 3.27 Å3/Da / Density % sol: 62.36 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.6
Details: PEG3350, MAGNESIUM ACETATE, BIS-TRIS, N-OCTYL TETRAOXYETHELYENE, tris-(2-carboxyethyl)phosphine hydrochloride , 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: 19-ID / Wavelength: 0.979 Å
DetectorType: SBC-2 / Detector: CCD / Date: Mar 5, 2002 / Details: Rosenbaum-Rock vertical focusing mirror
RadiationMonochromator: Rosenbaum-Rock high-resolution double-crystal sagittal focusing
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.7→30 Å / Num. obs: 44260 / % possible obs: 95.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 6.6 % / Rsym value: 0.085 / Net I/σ(I): 20.2
Reflection shellResolution: 2.7→2.8 Å / Redundancy: 2.7 % / Num. unique all: 3915 / Rsym value: 0.536 / % possible all: 84.6
Reflection
*PLUS
Lowest resolution: 20 Å / Num. obs: 44020 / % possible obs: 96.4 % / Redundancy: 6 % / Rmerge(I) obs: 0.091
Reflection shell
*PLUS
Highest resolution: 2.7 Å / Lowest resolution: 2.78 Å / % possible obs: 89.3 % / Rmerge(I) obs: 0.56

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
SCALEPACKdata scaling
SnBphasing
CNSrefinement
SHARPphasing
DENZOdata reduction
CNSphasing
RefinementMethod to determine structure: SAD/direct method / Resolution: 2.7→20 Å / Cor.coef. Fo:Fc: 0.908 / Cor.coef. Fo:Fc free: 0.879 / SU B: 17.389 / SU ML: 0.366 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: TLS / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.66 / ESU R Free: 0.357 / 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
Rfree0.288 1216 5.1 %RANDOM
Rwork0.244 ---
all0.246 22832 --
obs0.246 22706 96.45 %-
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: 39.163 Å2
Baniso -1Baniso -2Baniso -3
1-0.56 Å20.28 Å20 Å2
2--0.56 Å20 Å2
3----0.84 Å2
Refine analyzeLuzzati sigma a free: 0.36 Å
Refinement stepCycle: LAST / Resolution: 2.7→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4294 0 127 69 4490
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0214512
X-RAY DIFFRACTIONr_bond_other_d00.023962
X-RAY DIFFRACTIONr_angle_refined_deg1.8181.9466078
X-RAY DIFFRACTIONr_angle_other_deg0.7739213
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6643539
X-RAY DIFFRACTIONr_dihedral_angle_3_deg22.89515705
X-RAY DIFFRACTIONr_chiral_restr0.10.2636
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.025006
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02965
X-RAY DIFFRACTIONr_nbd_refined0.3740.31207
X-RAY DIFFRACTIONr_nbd_other0.3490.34697
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2040.5361
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.1150.515
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3650.328
X-RAY DIFFRACTIONr_symmetry_vdw_other0.410.3126
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.5650.54
X-RAY DIFFRACTIONr_symmetry_hbond_other0.5920.51
X-RAY DIFFRACTIONr_mcbond_it11.3091.52671
X-RAY DIFFRACTIONr_mcangle_it13.70324281
X-RAY DIFFRACTIONr_scbond_it20.05231841
X-RAY DIFFRACTIONr_scangle_it25.0984.51797
LS refinement shellResolution: 2.7→2.769 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.399 90
Rwork0.322 1467
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)
11.78160.29830.14041.0139-0.2990.8986-0.01150.2332-0.1086-0.07090.0090.07380.1536-0.15570.00250.28340.18350.03590.12010.00990.1428-6.31964.316524.7511
20.8155-0.14330.02260.78780.11390.750.02110.2159-0.0279-0.1179-0.01180.06050.0597-0.0695-0.00920.2520.15910.05710.13470.03660.1354-4.708865.650522.7514
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA7 - 1367 - 136
2X-RAY DIFFRACTION2AA137 - 594137 - 594
Software
*PLUS
Version: 5.1.24 / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.7 Å / Lowest resolution: 20 Å / % reflection Rfree: 5 % / Rfactor Rfree: 0.286
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.018
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg2.12

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