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- PDB-2ltq: High resolution structure of DsbB C41S by joint calculation with ... -

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Basic information

Entry
Database: PDB / ID: 2ltq
TitleHigh resolution structure of DsbB C41S by joint calculation with solid-state NMR and X-ray data
Components
  • Disulfide bond formation protein B
  • Fab fragment heavy chainFragment antigen-binding
  • Fab fragment light chainFragment antigen-binding
KeywordsMEMBRANE PROTEIN / OXIDOREDUCTASE / DISULFIDE BOND / REDOX-ACTIVE CENTER / CELL INNER MEMBRANE / CELL MEMBRANE / CHAPERONE / ELECTRON TRANSPORT / MEMBRANE / TRANSMEMBRANE / TRANSPORT
Function / homology
Function and homology information


oxidoreductase activity, acting on a sulfur group of donors, quinone or similar compound as acceptor / ubiquinone binding / protein-disulfide reductase activity / protein folding / response to heat / electron transfer activity / plasma membrane
Similarity search - Function
Bromodomain-like / DsbB-like / Disulphide bond formation protein DsbB/BdbC / Disulphide bond formation protein DsbB / DsbB-like superfamily / Disulfide bond formation protein DsbB / Immunoglobulins / Up-down Bundle / Immunoglobulin-like / Sandwich ...Bromodomain-like / DsbB-like / Disulphide bond formation protein DsbB/BdbC / Disulphide bond formation protein DsbB / DsbB-like superfamily / Disulfide bond formation protein DsbB / Immunoglobulins / Up-down Bundle / Immunoglobulin-like / Sandwich / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Ubiquinone-8 / Disulfide bond formation protein B
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Mus musculus (house mouse)
MethodSOLID-STATE NMR / simulated annealing
Model detailslowest energy, model 1
AuthorsTang, M. / Sperling, L.J. / Schwieters, C.D. / Nesbitt, A.E. / Gennis, R.B. / Rienstra, C.M.
CitationJournal: J.Mol.Biol. / Year: 2013
Title: Structure of the Disulfide Bond Generating Membrane Protein DsbB in the Lipid Bilayer.
Authors: Tang, M. / Nesbitt, A.E. / Sperling, L.J. / Berthold, D.A. / Schwieters, C.D. / Gennis, R.B. / Rienstra, C.M.
History
DepositionMay 30, 2012Deposition site: BMRB / Processing site: RCSB
Revision 1.0Feb 27, 2013Provider: repository / Type: Initial release
Revision 1.1May 22, 2013Group: Database references
Revision 2.0Jun 14, 2023Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Non-polymer description / Other / Source and taxonomy / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / database_2 / entity / entity_src_gen / entity_src_nat / pdbx_database_status / pdbx_entity_nonpoly / pdbx_nmr_software / pdbx_nonpoly_scheme / pdbx_unobs_or_zero_occ_atoms / struct_ref / struct_ref_seq / struct_ref_seq_dif / struct_site
Item: _atom_site.Cartn_x / _atom_site.Cartn_y ..._atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.name / _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.formula_weight / _entity.pdbx_description / _entity_src_gen.pdbx_beg_seq_num / _entity_src_gen.pdbx_end_seq_num / _entity_src_gen.pdbx_gene_src_gene / _entity_src_gen.pdbx_gene_src_scientific_name / _entity_src_gen.pdbx_seq_type / _entity_src_nat.pdbx_beg_seq_num / _entity_src_nat.pdbx_end_seq_num / _pdbx_database_status.status_code_nmr_data / _pdbx_entity_nonpoly.comp_id / _pdbx_entity_nonpoly.name / _pdbx_nmr_software.name / _pdbx_nonpoly_scheme.mon_id / _pdbx_nonpoly_scheme.pdb_mon_id / _struct_ref.pdbx_align_begin / _struct_ref_seq.db_align_end / _struct_ref_seq.pdbx_auth_seq_align_end / _struct_ref_seq.pdbx_db_accession / _struct_ref_seq.pdbx_strand_id / _struct_ref_seq.ref_id / _struct_ref_seq.seq_align_end / _struct_ref_seq_dif.align_id / _struct_ref_seq_dif.details / _struct_site.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: Disulfide bond formation protein B
B: Fab fragment light chain
C: Fab fragment heavy chain
D: Disulfide bond formation protein B
E: Fab fragment light chain
F: Fab fragment heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)141,7308
Polymers140,2766
Non-polymers1,4542
Water0
1
A: Disulfide bond formation protein B
B: Fab fragment light chain
C: Fab fragment heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,8654
Polymers70,1383
Non-polymers7271
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
D: Disulfide bond formation protein B
E: Fab fragment light chain
F: Fab fragment heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,8654
Polymers70,1383
Non-polymers7271
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 200structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Disulfide bond formation protein B / / Disulfide oxidoreductase


Mass: 20106.982 Da / Num. of mol.: 2 / Mutation: C8A,C41S,C49V
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria)
Strain: K12 / Gene: dsbB, roxB, ycgA, b1185, JW5182 / Production host: Escherichia coli (E. coli) / References: UniProt: P0A6M2
#2: Antibody Fab fragment light chain / Fragment antigen-binding


Mass: 26364.410 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Details: FAB FRAGMENT IS OBTAINED BY PAPAIN DIGESTION OF A SELECTED MONOCLONAL ANTIBODY
Source: (natural) Mus musculus (house mouse)
#3: Antibody Fab fragment heavy chain / Fragment antigen-binding


Mass: 23666.453 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Details: FAB FRAGMENT IS OBTAINED BY PAPAIN DIGESTION OF A SELECTED MONOCLONAL ANTIBODY
Source: (natural) Mus musculus (house mouse)
#4: Chemical ChemComp-UQ8 / Ubiquinone-8 / 2,3-dimethoxy-5-methyl-6-[(6E,10E,14E,18E,22E,26E)-3,7,11,15,19,23,27,31-octamethyldotriaconta-2,6,10,14,18,22,26,30-oc taen-1-yl]cyclohexa-2,5-diene-1,4-dione


Mass: 727.109 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C49H74O4

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Experimental details

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Experiment

ExperimentMethod: SOLID-STATE NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D CC DARR
1222D CC DARR
1332D CC DARR
1413D NCACX
1513D NCOCX
NMR detailsText: Chemical shifts assignments and CC correlations provide dihedral angle and distance restraints.

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Sample preparation

Details
Solution-IDContentsSolvent system
17 mg [U-100% 13C; U-100% 15N] DsbB, 2 mg DDM, 7 mg E. coli lipids, 90% H2O/10% D2O90% H2O/10% D2O
25 mg [2-13C-glycerol; U-15N] DsbB, 2 mg DDM, 7 mg E. coli lipids, 90% H2O/10% D2O90% H2O/10% D2O
34 mg [1,3-13C-glycerol; U-15N] DsbB, 2 mg DDM, 7 mg E. coli lipids, 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
7 mg/mLDsbB-1[U-100% 13C; U-100% 15N]1
2 mg/mLDDM-21
7 mg/mLE. coli lipids-31
5 mg/mLDsbB-4[2-13C-glycerol; U-15N]2
2 mg/mLDDM-52
7 mg/mLE. coli lipids-62
4 mg/mLDsbB-7[1,3-13C-glycerol; U-15N]3
2 mg/mLDDM-83
7 mg/mLE. coli lipids-93
Sample conditionspH: 7.8 / Pressure: ambient / Temperature: 261 K

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NMR measurement

Radiation wavelengthRelative weight: 1
NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA7501
Varian VXRSVarianVXRS5002

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Processing

NMR software
NameDeveloperClassification
SparkyGoddardchemical shift assignment
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorerefinement
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorestructure solution
TALOS+Shen, Cornilescu, Delaglio and Baxdata analysis
VnmrJVariancollection
RefinementMethod: simulated annealing / Software ordinal: 1
Details: JOINT CALCULATION OF DSBB C41S FAB WITH SOLID-STATE NMR RESTRAINTS AND X-RAY REFLECTIONS (X-RAY DATA ARE FROM PDB ID: 2ZUQ)
NMR constraintsNOE constraints total: 1334
NMR representativeSelection criteria: lowest energy
NMR ensembleAverage torsion angle constraint violation: 0 °
Conformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 10 / Maximum lower distance constraint violation: 0.51 Å / Maximum torsion angle constraint violation: 0 ° / Maximum upper distance constraint violation: 0.52 Å
NMR ensemble rmsDistance rms dev: 0.09 Å / Distance rms dev error: 0.001 Å

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