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- PDB-3m8b: Crystal structure of spin-labeled BtuB V10R1 in the apo state -

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Basic information

Entry
Database: PDB / ID: 3m8b
TitleCrystal structure of spin-labeled BtuB V10R1 in the apo state
ComponentsVitamin B12 transporter btuB
KeywordsTRANSPORT PROTEIN / beta barrel / R1 / spin label / Cell membrane / Cell outer membrane / Ion transport / Membrane / Metal-binding / Phage recognition / Porin / Receptor / TonB box / Transmembrane / Transport
Function / homology
Function and homology information


ABC-type vitamin B12 transporter activity / cobalamin transport / porin activity / pore complex / transmembrane transporter 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, beta-barrel domain / TonB-dependent receptor, plug domain / Maltoporin; Chain A / 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 receptor-like, beta-barrel ...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 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 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
Chem-MTN / Vitamin B12 transporter BtuB
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.44 Å
AuthorsFreed, D.M. / Horanyi, P.S. / Wiener, M.C. / Cafiso, D.S.
CitationJournal: Biophys.J. / Year: 2010
Title: Conformational exchange in a membrane transport protein is altered in protein crystals.
Authors: Freed, D.M. / Horanyi, P.S. / Wiener, M.C. / Cafiso, D.S.
History
DepositionMar 17, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 15, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jul 27, 2011Group: Non-polymer description
Revision 1.3Oct 26, 2011Group: Database references
Revision 1.4Feb 15, 2012Group: Derived calculations / Non-polymer description
Revision 1.5Nov 8, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software
Revision 1.6Sep 6, 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_conn_type
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_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_type.id
Revision 1.7Oct 30, 2024Group: Structure summary / Category: 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 transporter btuB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,89713
Polymers66,3901
Non-polymers2,50712
Water2,036113
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)81.290, 81.290, 226.562
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 transporter btuB / Cobalamin receptor / Outer membrane cobalamin translocator


Mass: 66390.195 Da / Num. of mol.: 1 / Mutation: V10R1A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: btuB, bfe, cer, dcrC, b3966, JW3938 / Production host: Escherichia coli (E. coli) / References: UniProt: P06129
#2: 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
#3: Chemical ChemComp-MTN / S-[(1-oxyl-2,2,5,5-tetramethyl-2,5-dihydro-1H-pyrrol-3-yl)methyl] methanesulfonothioate / MTSL


Mass: 264.385 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H18NO3S2
#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 113 / 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: 1

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Sample preparation

CrystalDensity Matthews: 3.25 Å3/Da / Density % sol: 62.11 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 6.6
Details: 2.5% PEG3350,20 mM Bis Tris, 150 mM Magnesium acetate, 10 mM C8E4, pH 6.6, VAPOR DIFFUSION, HANGING DROP, temperature 290K

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Data collection

DiffractionMean temperature: 90 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Nov 30, 2009
RadiationMonochromator: Si 220. Rosenbaum-Rock double-crystal monochromator: liquid nitrogen cooled; sagitally focusing 2nd crystal, Rosenbaum-Rock vertical focusing mirror
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionRedundancy: 9.6 % / Av σ(I) over netI: 26.29 / Number: 311539 / Rmerge(I) obs: 0.091 / Χ2: 1.52 / D res high: 2.4 Å / D res low: 50 Å / Num. obs: 32472 / % possible obs: 92.9
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
5.175099.610.0521.22710.3
4.15.1799.910.0751.3610.9
3.584.110010.1061.43710.9
3.263.5810010.1321.71610.6
3.023.2610010.1461.90510.2
2.853.0299.910.1731.729.9
2.72.8599.610.2191.6549.5
2.592.798.410.2771.4468.6
2.492.5990.810.3521.1867
2.42.4938.610.3831.0974.6
ReflectionResolution: 2.4→50 Å / Num. all: 32472 / Num. obs: 32472 / % possible obs: 92.9 % / Observed criterion σ(F): 6.9 / Observed criterion σ(I): 2 / Redundancy: 9.6 % / Rmerge(I) obs: 0.091 / Rsym value: 0.091 / Χ2: 1.52 / Net I/σ(I): 14.2
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.383 / Num. unique all: 1314 / Χ2: 1.097 / % possible all: 38.6

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 35.33 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å44.13 Å
Translation2.5 Å44.13 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASER2.1.4phasing
REFMACrefinement
PDB_EXTRACT3.1data extraction
MAR345SERGUIdata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1NQE, residue 10 deleted

1nqe


Resolution: 2.44→44.13 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.93 / WRfactor Rfree: 0.276 / WRfactor Rwork: 0.238 / Occupancy max: 1 / Occupancy min: 0.6 / FOM work R set: 0.846 / SU B: 14.043 / SU ML: 0.153 / SU R Cruickshank DPI: 0.335 / SU Rfree: 0.24 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.335 / ESU R Free: 0.24 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.248 1646 5.1 %RANDOM
Rwork0.219 ---
all0.264 30769 --
obs0.221 32415 97.59 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 119.76 Å2 / Biso mean: 30.191 Å2 / Biso min: 8.8 Å2
Baniso -1Baniso -2Baniso -3
1--0.04 Å2-0.02 Å20 Å2
2---0.04 Å20 Å2
3---0.07 Å2
Refinement stepCycle: LAST / Resolution: 2.44→44.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4329 0 163 113 4605
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.0214586
X-RAY DIFFRACTIONr_bond_other_d0.0040.023126
X-RAY DIFFRACTIONr_angle_refined_deg1.8391.9536185
X-RAY DIFFRACTIONr_angle_other_deg0.9543.0017538
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.8135545
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.69123.85226
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.6615669
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.8831529
X-RAY DIFFRACTIONr_chiral_restr0.1120.2643
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.025084
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02981
X-RAY DIFFRACTIONr_mcbond_it1.0521.52695
X-RAY DIFFRACTIONr_mcbond_other0.2211.51146
X-RAY DIFFRACTIONr_mcangle_it1.98624318
X-RAY DIFFRACTIONr_scbond_it3.04831891
X-RAY DIFFRACTIONr_scangle_it4.9784.51867
LS refinement shellResolution: 2.44→2.504 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.39 108 -
Rwork0.346 1797 -
all-1905 -
obs-1797 79.34 %
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)
11.73050.0280.06671.64490.24041.3702-0.0398-0.2366-0.16060.08430.0163-0.05870.12920.08610.02350.2192-0.12350.05850.1329-0.01530.1218-34.9748-5.826613.1805
21.07870.2343-0.08070.87630.03991.12370.0582-0.2419-0.06060.1019-0.0749-0.04790.04910.10190.01660.1747-0.11840.06850.1325-0.03580.0814-36.4715-5.03615.3942
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A7 - 132
2X-RAY DIFFRACTION2A137 - 594

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