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- PDB-1ujw: Structure of the complex between BtuB and Colicin E3 Receptor bin... -

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Basic information

Entry
Database: PDB / ID: 1ujw
TitleStructure of the complex between BtuB and Colicin E3 Receptor binding domain
Components
  • Colicin E3
  • Vitamin B12 receptor
KeywordsTRANSPORT PROTEIN/HYDROLASE / beta-barrel / coiled-coil / TRANSPORT PROTEIN-HYDROLASE COMPLEX
Function / homology
Function and homology information


negative regulation of ion transmembrane transporter activity / ABC-type vitamin B12 transporter activity / extrachromosomal circular DNA / cobalamin transport / transmembrane transporter complex / porin activity / pore complex / cell outer membrane / ribosome binding / Lyases; Phosphorus-oxygen lyases ...negative regulation of ion transmembrane transporter activity / ABC-type vitamin B12 transporter activity / extrachromosomal circular DNA / cobalamin transport / transmembrane transporter complex / porin activity / pore complex / cell outer membrane / ribosome binding / Lyases; Phosphorus-oxygen lyases / monoatomic ion transmembrane transport / endonuclease activity / killing of cells of another organism / transmembrane transporter binding / tRNA binding / rRNA binding / defense response to bacterium / lyase activity / protein domain specific binding / calcium ion binding / extracellular region / membrane
Similarity search - Function
Helix Hairpins / Colicin E3-like ribonuclease domain / Colicin E3-like ribonuclease domain superfamily / Cytotoxic / TonB-dependent vitamin B12 transporter BtuB / Colicin, receptor domain / Coiled-coil receptor-binding R-domain of colicin E2 / Cloacin colicin family / Colicin-like bacteriocin tRNase domain / TonB-dependent receptor (TBDR) proteins signature 1. ...Helix Hairpins / Colicin E3-like ribonuclease domain / Colicin E3-like ribonuclease domain superfamily / Cytotoxic / TonB-dependent vitamin B12 transporter BtuB / Colicin, receptor domain / Coiled-coil receptor-binding R-domain of colicin E2 / Cloacin colicin family / Colicin-like bacteriocin tRNase domain / TonB-dependent receptor (TBDR) proteins signature 1. / TonB-dependent receptor, plug domain / Pyosin/cloacin translocation domain / Pyosin/cloacin translocation domain superfamily / TonB box, conserved site / Ferric Hydroxamate Uptake Protein; Chain A, domain 1 / TonB-dependent receptor, beta-barrel domain / TonB-dependent receptor, conserved site / TonB-dependent receptor (TBDR) proteins signature 2. / Maltoporin; Chain A / 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 / Helix Hairpins / Beta Barrel / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
ACETOACETIC ACID / Chem-GP1 / 3-OXO-PENTADECANOIC ACID / Colicin E3 / Vitamin B12 transporter BtuB
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.75 Å
AuthorsKurisu, G. / Zakharov, S.D. / Zhalnina, M.V. / Bano, S. / Eroukova, V.Y. / Rokitskaya, T.I. / Antonenko, Y.N. / Wiener, M.C. / Cramer, W.A.
CitationJournal: NAT.STRUCT.BIOL. / Year: 2003
Title: The structure of BtuB with bound colicin E3 R-domain implies a translocon
Authors: Kurisu, G. / Zakharov, S.D. / Zhalnina, M.V. / Bano, S. / Eroukova, V.Y. / Rokitskaya, T.I. / Antonenko, Y.N. / Wiener, M.C. / Cramer, W.A.
History
DepositionAug 12, 2003Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 25, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_label_atom_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Oct 25, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag
Remark 650HELIX DETERMINATION METHOD: AUTHOR DETERMINED

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Vitamin B12 receptor
B: Colicin E3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,97322
Polymers81,4972
Non-polymers3,47620
Water18010
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7220 Å2
ΔGint-32 kcal/mol
Surface area33390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.933, 80.098, 233.595
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 2 types, 2 molecules AB

#1: Protein Vitamin B12 receptor / Cobalamin Transporter


Mass: 66386.180 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Plasmid: pJC3 / Production host: Escherichia coli (E. coli) / References: UniProt: P06129
#2: Protein Colicin E3 / Colicin E3 A chain / Ribonuclease


Mass: 15110.648 Da / Num. of mol.: 1 / Fragment: R-domain(residues 314-448)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Plasmid: pET-216(+) / Production host: Escherichia coli (E. coli) / References: UniProt: P00646

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Sugars , 1 types, 2 molecules

#3: Sugar ChemComp-GP1 / 2-amino-2-deoxy-1-O-phosphono-alpha-D-glucopyranose / GLUCOSAMINE 1-PHOSPHATE / 1-O-phosphono-alpha-D-glucosamine / 2-amino-2-deoxy-1-O-phosphono-alpha-D-glucose / 2-amino-2-deoxy-1-O-phosphono-D-glucose / 2-amino-2-deoxy-1-O-phosphono-glucose


Type: D-saccharide / Mass: 259.151 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C6H14NO8P
IdentifierTypeProgram
a-D-Glcp1PO3NIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0

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Non-polymers , 5 types, 28 molecules

#4: Chemical ChemComp-LIM / 3-OXO-PENTADECANOIC ACID


Mass: 256.381 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C15H28O3
#5: Chemical
ChemComp-LDA / LAURYL DIMETHYLAMINE-N-OXIDE


Mass: 229.402 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C14H31NO / Comment: LDAO, detergent*YM
#6: Chemical ChemComp-AAE / ACETOACETIC ACID


Mass: 102.089 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H6O3
#7: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C3H8O3
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 10 / 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: 4.5 Å3/Da / Density % sol: 72.44 %
Crystal grow
*PLUS
Temperature: 20 ℃ / pH: 6.5 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
110 mMMES1droppH6.5
20.1 M1dropNaCl
30.1 %(w/v)LDAO1drop
40.1 MADA1reservoirpH6.0
50.9 Mammonium sulfate1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM
DetectorType: SBC / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.75→50 Å / Num. obs: 37175
Reflection
*PLUS
Lowest resolution: 35.5 Å / % possible obs: 96.7 % / Redundancy: 3.8 % / Num. measured all: 139699 / Rmerge(I) obs: 0.084
Reflection shell
*PLUS
Highest resolution: 2.75 Å / Lowest resolution: 2.85 Å / % possible obs: 91.1 % / Rmerge(I) obs: 0.295 / Mean I/σ(I) obs: 2.9

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
HKL-2000data reduction
HKL-2000data scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1NQE

1nqe


Resolution: 2.75→37.88 Å / Cor.coef. Fo:Fc: 0.916 / Cor.coef. Fo:Fc free: 0.876 / SU B: 14.189 / SU ML: 0.275 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.469 / ESU R Free: 0.333 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.293 1864 5 %RANDOM
Rwork0.244 ---
all0.247 ---
obs0.247 35281 96.71 %-
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: 33.257 Å2
Baniso -1Baniso -2Baniso -3
1--5.66 Å20 Å20 Å2
2--6.6 Å20 Å2
3----0.95 Å2
Refinement stepCycle: LAST / Resolution: 2.75→37.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5472 0 232 10 5714
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0215816
X-RAY DIFFRACTIONr_bond_other_d0.0020.025103
X-RAY DIFFRACTIONr_angle_refined_deg1.8681.9597851
X-RAY DIFFRACTIONr_angle_other_deg0.936311889
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.5745689
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.160.2812
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.026442
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021224
X-RAY DIFFRACTIONr_nbd_refined0.2250.21251
X-RAY DIFFRACTIONr_nbd_other0.2490.26191
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.0960.23760
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1470.298
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1020.28
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2280.266
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_mcbond_it0.51.53412
X-RAY DIFFRACTIONr_mcangle_it0.96925452
X-RAY DIFFRACTIONr_scbond_it1.75432404
X-RAY DIFFRACTIONr_scangle_it2.7824.52399
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.75→2.821 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.4 142
Rwork0.337 2370
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)
14.0485-0.85070.562.4505-0.58652.89040.11030.26890.25050.1042-0.0086-0.0295-0.81510.1827-0.10160.3741-0.06270.03230.17960.08190.047911.46137.101108.195
21.5866-0.16160.10971.0422-0.20743.14370.03570.37470.2645-0.07050.00950.0504-0.65820.1207-0.04520.3478-0.00490.02870.3450.09420.047510.11836.383104.122
30.2135-0.3343-0.79786.64735.95316.15730.11260.3052-0.13840.00610.3562-0.59030.35580.0013-0.46880.66680.0519-0.15260.821-0.11030.297513.3968.359.016
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA4 - 1334 - 133
2X-RAY DIFFRACTION2AA134 - 594134 - 594
3X-RAY DIFFRACTION3BB323 - 43810 - 125
Refinement
*PLUS
Lowest resolution: 35.5 Å / % reflection Rfree: 5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.016
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg1.868

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