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- PDB-3e9j: Structure of the charge-transfer intermediate of the transmembran... -

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Basic information

Entry
Database: PDB / ID: 3e9j
TitleStructure of the charge-transfer intermediate of the transmembrane redox catalyst DsbB
Components
  • Thiol/disulfide oxidoreductase DsbA
  • Thiol/disulfide oxidoreductase DsbB
KeywordsOXIDOREDUCTASE / membrane protein complex / mechanism of disulfide bond formation / oxidative protein folding in Escherichia coli periplasm / X-ray crystal structure / charge transfer reaction intermediate / four helix bundle / Periplasm / 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 / cellular response to antibiotic / protein disulfide isomerase activity / ubiquinone binding / protein-disulfide reductase activity / protein folding / outer membrane-bounded periplasmic space / 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 / Thiol:disulphide interchange protein DsbA/DsbL / : / DSBA-like thioredoxin domain ...Bromodomain-like / DsbB-like / Disulphide bond formation protein DsbB/BdbC / Disulphide bond formation protein DsbB / DsbB-like superfamily / : / Disulfide bond formation protein DsbB / Thiol:disulphide interchange protein DsbA/DsbL / : / DSBA-like thioredoxin domain / DSBA-like thioredoxin domain / Thioredoxin, conserved site / Thioredoxin family active site. / Thioredoxin domain profile. / Thioredoxin domain / Glutaredoxin / Glutaredoxin / Thioredoxin-like superfamily / Up-down Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
UBIQUINONE-1 / Disulfide bond formation protein B / Thiol:disulfide interchange protein DsbA
Similarity search - Component
Biological speciesEscherichia coli K12 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.7 Å
AuthorsMalojcic, G. / Owen, R.L. / Glockshuber, R.
CitationJournal: Febs Lett. / Year: 2008
Title: Preparation and structure of the charge-transfer intermediate of the transmembrane redox catalyst DsbB.
Authors: Malojcic, G. / Owen, R.L. / Grimshaw, J.P. / Glockshuber, R.
History
DepositionAug 22, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 25, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 20, 2021Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Aug 30, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 1.4Oct 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
B: Thiol/disulfide oxidoreductase DsbA
C: Thiol/disulfide oxidoreductase DsbB
E: Thiol/disulfide oxidoreductase DsbA
F: Thiol/disulfide oxidoreductase DsbB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,6506
Polymers84,1504
Non-polymers5012
Water00
1
B: Thiol/disulfide oxidoreductase DsbA
C: Thiol/disulfide oxidoreductase DsbB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,3253
Polymers42,0752
Non-polymers2501
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1310 Å2
ΔGint-13 kcal/mol
Surface area18680 Å2
MethodPISA
2
E: Thiol/disulfide oxidoreductase DsbA
F: Thiol/disulfide oxidoreductase DsbB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,3253
Polymers42,0752
Non-polymers2501
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1320 Å2
ΔGint-13 kcal/mol
Surface area18640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.305, 103.105, 125.826
Angle α, β, γ (deg.)90.00, 91.16, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11B
21E
12C
22F

NCS domain segments:

Component-ID: 1 / Beg auth comp-ID: ALA / Beg label comp-ID: ALA / Refine code: 1

Dom-IDEns-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11LYSLYSBA1 - 1881 - 188
21LYSLYSEC1 - 1881 - 188
12UQ1UQ1CB - E14 - 50114
22UQ1UQ1FD - F14 - 50114

NCS ensembles :
ID
1
2
3

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Components

#1: Protein Thiol/disulfide oxidoreductase DsbA / Thiol:disulfide interchange protein dsbA


Mass: 21122.959 Da / Num. of mol.: 2 / Mutation: C33A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K12 (bacteria) / Strain: BL21(DE3) / Gene: dsbA, dsf, ppfA, b3860, JW3832 / Plasmid: pDsbA / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P0AEG4, Oxidoreductases; Acting on a sulfur group of donors; With a disulfide as acceptor
#2: Protein Thiol/disulfide oxidoreductase DsbB / Disulfide bond formation protein B


Mass: 20951.928 Da / Num. of mol.: 2 / Mutation: C8A, C49V
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K12 (bacteria) / Strain: HM125 / Gene: dsbB, roxB, ycgA, b1185, JW5182 / Plasmid: pDsbB / Production host: Escherichia coli (E. coli) / Strain (production host): HM125
References: UniProt: P0A6M2, Oxidoreductases; Acting on a sulfur group of donors; With a quinone or similar compound as acceptor
#3: Chemical ChemComp-UQ1 / UBIQUINONE-1


Mass: 250.290 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H18O4
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: 5.110001 Å3/Da / Density % sol: 75.929558 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8.9
Details: 23% PEG550 MME, 50 mM Tris pH 8.9, 1.0 M ammonium formate, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.92 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Aug 26, 2006
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 3.7→125 Å / Num. obs: 18142 / % possible obs: 98 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 3 / Redundancy: 3.1 % / Rsym value: 0.072 / Net I/σ(I): 9.9
Reflection shellResolution: 3.7→3.9 Å / Redundancy: 3.1 % / Mean I/σ(I) obs: 2 / Rsym value: 0.436 / % possible all: 99.1

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
CLARAdata collection
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2HI7

2hi7


Resolution: 3.7→125.99 Å / Cor.coef. Fo:Fc: 0.893 / Cor.coef. Fo:Fc free: 0.86 / SU B: 67.62 / SU ML: 0.953 / Cross valid method: THROUGHOUT / ESU R: 2.324 / ESU R Free: 0.79 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.37903 726 4.1 %RANDOM
Rwork0.33733 ---
obs0.33893 17000 97.22 %-
all-18142 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 160.416 Å2
Baniso -1Baniso -2Baniso -3
1--23.32 Å20 Å2-2.51 Å2
2--20.62 Å20 Å2
3---2.6 Å2
Refinement stepCycle: LAST / Resolution: 3.7→125.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5112 0 36 0 5148
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0225286
X-RAY DIFFRACTIONr_bond_other_d0.0020.023466
X-RAY DIFFRACTIONr_angle_refined_deg1.4181.967190
X-RAY DIFFRACTIONr_angle_other_deg0.97338484
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.535638
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.47724.455220
X-RAY DIFFRACTIONr_dihedral_angle_3_deg22.54915864
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.4671514
X-RAY DIFFRACTIONr_chiral_restr0.0740.2806
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.025774
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021076
X-RAY DIFFRACTIONr_nbd_refined0.2680.21673
X-RAY DIFFRACTIONr_nbd_other0.2190.23940
X-RAY DIFFRACTIONr_nbtor_refined0.1980.22511
X-RAY DIFFRACTIONr_nbtor_other0.0940.22669
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2060.2186
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.1110.28
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3880.29
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1360.23
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Refine-ID: X-RAY DIFFRACTION / Type: tight positional / Weight position: 0.05

Ens-IDAuth asym-IDNumberRms dev position (Å)
1B24790.03
2C18280.02
LS refinement shellResolution: 3.7→3.796 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.597 45 -
Rwork0.507 1251 -
obs--98.33 %

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