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- PDB-3m8d: Crystal structure of spin-labeled BtuB V10R1 with bound calcium a... -

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Basic information

Entry
Database: PDB / ID: 3m8d
TitleCrystal structure of spin-labeled BtuB V10R1 with bound calcium and cyanocobalamin
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 / 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 / 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 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_conn_type
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.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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Vitamin B12 transporter btuB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,97012
Polymers66,3901
Non-polymers3,58011
Water1,36976
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)82.051, 82.051, 224.457
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Vitamin B12 transporter btuB


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

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Non-polymers , 5 types, 87 molecules

#2: Chemical ChemComp-CNC / CYANOCOBALAMIN / Cyanocobalamin


Mass: 1356.373 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C63H89CoN14O14P / Comment: medication*YM
#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: Chemical ChemComp-MTN / S-[(1-oxyl-2,2,5,5-tetramethyl-2,5-dihydro-1H-pyrrol-3-yl)methyl] methanesulfonothioate / MTSL / MTSL


Mass: 264.385 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H18NO3S2
#5: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 76 / 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: 3.28 Å3/Da / Density % sol: 62.46 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 6.6
Details: 2.5% PEG3350, 150 mM calcium chloride, 20 mM Bis tris, 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
ReflectionResolution: 2.44→50 Å / Num. all: 32358 / Num. obs: 32358 / % possible obs: 96.7 % / Observed criterion σ(F): 4.9 / Observed criterion σ(I): 2 / Redundancy: 9.1 % / Rmerge(I) obs: 0.121 / Χ2: 1.653 / Net I/σ(I): 11.1
Reflection shellResolution: 2.44→2.54 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.458 / Num. unique all: 2370 / Χ2: 1.3 / % possible all: 72.4

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 36.85 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å44.04 Å
Translation2.5 Å44.04 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 / Resolution: 2.44→44.04 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.913 / WRfactor Rfree: 0.303 / WRfactor Rwork: 0.249 / Occupancy max: 1 / Occupancy min: 0.7 / FOM work R set: 0.827 / SU B: 17.249 / SU ML: 0.192 / SU R Cruickshank DPI: 0.375 / SU Rfree: 0.275 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.375 / ESU R Free: 0.275 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.275 1647 5.1 %RANDOM
Rwork0.226 ---
all0.279 30642 --
obs0.229 32289 96.57 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 123.94 Å2 / Biso mean: 37.685 Å2 / Biso min: 12.45 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å20 Å20 Å2
2---0.01 Å20 Å2
3---0.01 Å2
Refinement stepCycle: LAST / Resolution: 2.44→44.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4552 0 234 76 4862
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0214901
X-RAY DIFFRACTIONr_bond_other_d0.0010.023271
X-RAY DIFFRACTIONr_angle_refined_deg2.0371.9766660
X-RAY DIFFRACTIONr_angle_other_deg0.9693.0017884
X-RAY DIFFRACTIONr_dihedral_angle_1_deg9.0255581
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.67423.803234
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.3515681
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.721531
X-RAY DIFFRACTIONr_chiral_restr0.1070.2688
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.025483
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021046
X-RAY DIFFRACTIONr_mcbond_it0.8991.52864
X-RAY DIFFRACTIONr_mcbond_other0.1861.51212
X-RAY DIFFRACTIONr_mcangle_it1.64524584
X-RAY DIFFRACTIONr_scbond_it2.51432037
X-RAY DIFFRACTIONr_scangle_it4.0144.52076
LS refinement shellResolution: 2.442→2.505 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.385 74 -
Rwork0.361 1556 -
all-1630 -
obs--67.33 %
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)
11.5059-0.3301-0.64671.8189-0.7962.5488-0.1152-0.16710.06150.36930.0687-0.1509-0.19430.1370.04650.08190.027-0.04720.43480.1560.20521.5576-27.7695-24.2165
21.0934-0.0173-0.08381.0818-0.12471.0196-0.1201-0.15590.10490.29050.0921-0.0855-0.18380.02710.0280.11680.0574-0.03070.41160.17050.200820.8979-29.319-19.8176
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A7 - 132
2X-RAY DIFFRACTION2A137 - 594

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