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- PDB-5qkp: Group deposition of library data - Crystal Structure of EcDsbA af... -

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Basic information

Entry
Database: PDB / ID: 5qkp
TitleGroup deposition of library data - Crystal Structure of EcDsbA after initial refinement with no ligand modelled (structure A7_3)
ComponentsThiol:disulfide interchange protein
KeywordsOXIDOREDUCTASE / DISULFIDE OXIDOREDUCTASE / REDOX PROTEIN / DSBA
Function / homology
Function and homology information


cellular response to antibiotic / protein disulfide isomerase activity / protein-disulfide reductase activity / outer membrane-bounded periplasmic space / periplasmic space / oxidoreductase activity
Similarity search - Function
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 ...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 / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Thiol:disulfide interchange protein / Thiol:disulfide interchange protein DsbA
Similarity search - Component
Biological speciesEscherichia coli K-12 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.881 Å
AuthorsIlyichova, O.V. / Bentley, M.R. / Doak, B.C. / Scanlon, M.J.
CitationJournal: J.Med.Chem. / Year: 2020
Title: Rapid Elaboration of Fragments into Leads by X-ray Crystallographic Screening of Parallel Chemical Libraries (REFiLX).
Authors: Bentley, M.R. / Ilyichova, O.V. / Wang, G. / Williams, M.L. / Sharma, G. / Alwan, W.S. / Whitehouse, R.L. / Mohanty, B. / Scammells, P.J. / Heras, B. / Martin, J.L. / Totsika, M. / Capuano, ...Authors: Bentley, M.R. / Ilyichova, O.V. / Wang, G. / Williams, M.L. / Sharma, G. / Alwan, W.S. / Whitehouse, R.L. / Mohanty, B. / Scammells, P.J. / Heras, B. / Martin, J.L. / Totsika, M. / Capuano, B. / Doak, B.C. / Scanlon, M.J.
History
DepositionJan 27, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 5, 2020Provider: repository / Type: Initial release
Revision 1.1Jul 8, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jul 22, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Oct 30, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Thiol:disulfide interchange protein
B: Thiol:disulfide interchange protein


Theoretical massNumber of molelcules
Total (without water)42,3102
Polymers42,3102
Non-polymers00
Water4,089227
1
A: Thiol:disulfide interchange protein


Theoretical massNumber of molelcules
Total (without water)21,1551
Polymers21,1551
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Thiol:disulfide interchange protein


Theoretical massNumber of molelcules
Total (without water)21,1551
Polymers21,1551
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)117.926, 64.460, 74.638
Angle α, β, γ (deg.)90.000, 125.830, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-324-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A and segid A
21chain B and segid B

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111chain A and segid AA0
211chain B and segid BB0

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Components

#1: Protein Thiol:disulfide interchange protein


Mass: 21155.025 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Gene: dsbA / Plasmid: B0013 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A0A073FPA6, UniProt: P0AEG4*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 227 / Source method: isolated from a natural source / Formula: H2O
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: 2.72 Å3/Da / Density % sol: 54.75 % / Mosaicity: 0.22 °
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.1
Details: 11-13% PEG 8000 5-7.5% GLYCEROL 1 MM CUCL2 100 MM SODIUM CACODYLATE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Apr 18, 2018
RadiationMonochromator: DOUBLE SI WITH SAGITTALY BENT SECOND CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.88→34.81 Å / Num. obs: 35094 / % possible obs: 95.1 % / Redundancy: 4.2 % / CC1/2: 0.999 / Rmerge(I) obs: 0.039 / Rpim(I) all: 0.022 / Rrim(I) all: 0.045 / Net I/σ(I): 14.3 / Num. measured all: 148115 / Scaling rejects: 1
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.88-1.924.10.571598614470.7480.3160.6541.859.7
9.02-34.813.70.0212323310.9990.0120.02338.593.3

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
PHENIX1.9_1692refinement
XDSdata reduction
Aimless0.5.32data scaling
MOLREPphasing
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.881→34.805 Å / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 0.31 / Phase error: 34.37 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.261 823 2.37 %
Rwork0.2294 33865 -
obs0.2303 34688 93.77 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 141.51 Å2 / Biso mean: 46.8002 Å2 / Biso min: 20.79 Å2
Refinement stepCycle: final / Resolution: 1.881→34.805 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2956 0 0 227 3183
Biso mean---45.07 -
Num. residues----376
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0093022
X-RAY DIFFRACTIONf_angle_d1.2944084
X-RAY DIFFRACTIONf_chiral_restr0.052444
X-RAY DIFFRACTIONf_plane_restr0.006532
X-RAY DIFFRACTIONf_dihedral_angle_d16.0481102
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A1686X-RAY DIFFRACTION4.772TORSIONAL
12B1686X-RAY DIFFRACTION4.772TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 6

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.8814-1.99920.37611140.32414898501282
1.9992-2.15360.32931500.29295747589796
2.1536-2.37030.29841410.27895809595097
2.3703-2.71310.29241290.26765822595197
2.7131-3.41780.25121210.23865805592696
3.4178-34.81120.23441680.18625784595295

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