[English] 日本語
Yorodumi
- PDB-2gsk: Structure of the BtuB:TonB Complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2gsk
TitleStructure of the BtuB:TonB Complex
Components
  • Vitamin B12 transporter btuB
  • protein TONB
KeywordsSIGNALING PROTEIN/MEMBRANE PROTEIN / OUTER-MEMBRANE ACTIVE TRANSPORT / BETA-BARREL / TONB / MEMBRANE PROTEIN / SIGNALING PROTEIN-MEMBRANE PROTEIN COMPLEX
Function / homology
Function and homology information


receptor-mediated bacteriophage irreversible attachment to host cell / colicin transport / ABC-type vitamin B12 transporter activity / energy transducer activity / cell envelope / cobalamin transport / siderophore transport / intracellular monoatomic cation homeostasis / plasma membrane protein complex / transmembrane transporter complex ...receptor-mediated bacteriophage irreversible attachment to host cell / colicin transport / ABC-type vitamin B12 transporter activity / energy transducer activity / cell envelope / cobalamin transport / siderophore transport / intracellular monoatomic cation homeostasis / plasma membrane protein complex / transmembrane transporter complex / porin activity / pore complex / monoatomic ion transmembrane transport / cell outer membrane / transmembrane transport / protein transport / outer membrane-bounded periplasmic space / intracellular iron ion homeostasis / protein domain specific binding / calcium ion binding / membrane / plasma membrane
Similarity search - Function
TolA/TonB C-terminal domain / TonB / TonB polyproline region / TonB-dependent vitamin B12 transporter BtuB / TonB C-terminal domain profile. / Gram-negative bacterial TonB protein / TonB, C-terminal / Gram-negative bacterial TonB protein C-terminal / TonB/TolA, C-terminal / TonB-dependent receptor (TBDR) proteins signature 1. ...TolA/TonB C-terminal domain / TonB / TonB polyproline region / TonB-dependent vitamin B12 transporter BtuB / TonB C-terminal domain profile. / Gram-negative bacterial TonB protein / TonB, C-terminal / Gram-negative bacterial TonB protein C-terminal / TonB/TolA, C-terminal / 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 / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
CYANOCOBALAMIN / HEXANE / N-OCTANE / Protein TonB / Vitamin B12 transporter BtuB / Protein TonB
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsShultis, D.D. / Purdy, M.P. / Banchs, C.N. / Wiener, M.C.
Citation
Journal: Science / Year: 2006
Title: Outer membrane active transport: structure of the BtuB:TonB complex
Authors: Shultis, D.D. / Purdy, M.D. / Banchs, C.N. / Wiener, M.C.
#1: Journal: Acta Crystallogr.,Sect.F / Year: 2006
Title: Crystallization and preliminary x-ray crystallographic analysis of the Escherichia coli outer membrane cobalamin transporter BtuB in complex with the carboxy-terminal domain of TonB
Authors: Shultis, D.D. / Purdy, M.D. / Banchs, C.N. / Wiener, M.C.
History
DepositionApr 26, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 13, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software
Revision 1.4Nov 1, 2017Group: Refinement description / Category: pdbx_refine_tls
Item: _pdbx_refine_tls.origin_x / _pdbx_refine_tls.origin_y / _pdbx_refine_tls.origin_z
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_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 / _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 30, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Vitamin B12 transporter btuB
B: protein TONB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,07214
Polymers75,2022
Non-polymers2,86912
Water4,936274
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5090 Å2
ΔGint-5 kcal/mol
Surface area30360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.340, 82.439, 122.632
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
DetailsTHE BIOLOGICAL ASSEMBLY IS A 1:1 COMPLEX OF BTUB AND TONB, WITH THE PHYSIOLOGICAL INTERFACE BETWEEN BTUB RESIDUES 6-12 AND TONB RESIDUES 158-171 AND 225-232.

-
Components

-
Protein , 2 types, 2 molecules AB

#1: Protein Vitamin B12 transporter btuB / BTUB / Cobalamin receptor / Outer membrane cobalamin translocator


Mass: 65954.797 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: btuB, bfe, cer, dcrC / Plasmid: PET22B / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)PLYSS / References: UniProt: P06129
#2: Protein protein TONB


Mass: 9247.701 Da / Num. of mol.: 1 / Fragment: C-TERMINAL DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: tonB, exbA / Plasmid: PGEX4T1 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P94739, UniProt: P02929*PLUS

-
Non-polymers , 6 types, 286 molecules

#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-CNC / CYANOCOBALAMIN / Cyanocobalamin


Mass: 1356.373 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C63H89CoN14O14P / Comment: medication*YM
#5: Chemical
ChemComp-LDA / LAURYL DIMETHYLAMINE-N-OXIDE / Lauryldimethylamine oxide


Mass: 229.402 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C14H31NO / Comment: LDAO, detergent*YM
#6: Chemical ChemComp-OCT / N-OCTANE / Octane


Mass: 114.229 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C8H18
#7: Chemical ChemComp-HEX / HEXANE / Hexane


Mass: 86.175 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 274 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.5 Å3/Da / Density % sol: 50.75 %
Crystal growTemperature: 288 K / pH: 5.1
Details: 30% (v/v) PEG 300, 0.1M sodium acetate , pH 5.1, VAPOR DIFFUSION, SITTING DROP, temperature 288K, pH 5.10

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 9, 2005
RadiationMonochromator: SAGITALLY FOCUSED SI(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.098→40 Å / Num. obs: 44005 / % possible obs: 98.2 % / Observed criterion σ(I): 0 / Redundancy: 4.6 % / Rmerge(I) obs: 0.078 / Net I/σ(I): 11.9
Reflection shellResolution: 2.1→2.18 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.436 / % possible all: 90.5

-
Processing

Software
NameVersionClassification
MAR345data collection
SERGUIdata collection
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMAC5.2refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1NQH

1nqh


Resolution: 2.1→40 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.924 / SU B: 9.588 / SU ML: 0.14 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.221 / ESU R Free: 0.195 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.251 1191 2.7 %RANDOM
Rwork0.196 ---
all0.197 43953 --
obs0.197 43953 98.1 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 28.33 Å2
Baniso -1Baniso -2Baniso -3
1-0.94 Å20 Å20 Å2
2---0.27 Å20 Å2
3----0.67 Å2
Refinement stepCycle: LAST / Resolution: 2.1→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5194 0 190 274 5658
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0250.0215512
X-RAY DIFFRACTIONr_bond_other_d0.0020.023663
X-RAY DIFFRACTIONr_angle_refined_deg2.2231.9667501
X-RAY DIFFRACTIONr_angle_other_deg1.0438853
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.4545669
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.59423.837258
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.81315779
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.6071533
X-RAY DIFFRACTIONr_chiral_restr0.1270.2788
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.026216
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021176
X-RAY DIFFRACTIONr_nbd_refined0.2110.2879
X-RAY DIFFRACTIONr_nbd_other0.2150.23726
X-RAY DIFFRACTIONr_nbtor_refined0.190.22517
X-RAY DIFFRACTIONr_nbtor_other0.0980.23154
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2030.2295
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.140.21
X-RAY DIFFRACTIONr_metal_ion_refined0.1380.29
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2570.211
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2720.252
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0730.22
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.2811.53376
X-RAY DIFFRACTIONr_mcbond_other0.3771.51389
X-RAY DIFFRACTIONr_mcangle_it1.9725286
X-RAY DIFFRACTIONr_scbond_it3.24932493
X-RAY DIFFRACTIONr_scangle_it4.4944.52215
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.1→2.15 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.273 68 -
Rwork0.205 2764 -
obs--87.27 %
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)
10.6156-0.03550.04050.59070.01870.31520.00690.07840.00080.02630.0212-0.0335-0.00080.0025-0.02810.0246-0.00070.0098-0.05490.0095-0.133133.2293.466-13.083
20.73820.1594-0.25510.38820.18590.89380.0220.03840.07130.1040.0102-0.01-0.0202-0.0261-0.03220.07250.0074-0.0024-0.07090.0099-0.057531.5213.289-7.21
33.7135-1.94732.42943.0905-1.40094.4412-0.0885-0.00910.09830.19360.0748-0.45580.04110.35850.01370.04160.0099-0.0209-0.0325-0.011-0.067428.369-6.617.799
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA134 - 594130 - 590
2X-RAY DIFFRACTION2AA5 - 1331 - 129
3X-RAY DIFFRACTION3BB153 - 2331 - 81

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more