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

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Basic information

Entry
Database: PDB / ID: 5qmz
TitleGroup deposition of library data - Crystal Structure of EcDsbA after initial refinement with no ligand modelled (structure G5_1)
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 / Thioredoxin-like superfamily ...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: 2.084 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

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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
Water2,900161
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)118.131, 64.025, 74.594
Angle α, β, γ (deg.)90.000, 125.870, 90.000
Int Tables number5
Space group name H-MC121
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 / Water


Mass: 18.015 Da / Num. of mol.: 161 / 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: 2.7 Å3/Da / Density % sol: 54.47 % / Mosaicity: 0.27 °
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: 2.08→47.86 Å / Num. obs: 26853 / % possible obs: 98.8 % / Redundancy: 4.1 % / CC1/2: 0.998 / Rmerge(I) obs: 0.068 / Rpim(I) all: 0.038 / Rrim(I) all: 0.079 / Net I/σ(I): 9.9 / Num. measured all: 110990
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
2.08-2.144.10.784827120120.6970.4360.8981.495.5
9.07-47.863.70.02512543400.9980.0150.02929.894.9

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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: 2.084→47.865 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 0.32 / Phase error: 28.29 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2624 1012 3.89 %
Rwork0.2322 25018 -
obs0.2334 26030 95.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 145.98 Å2 / Biso mean: 48.7987 Å2 / Biso min: 20.72 Å2
Refinement stepCycle: final / Resolution: 2.084→47.865 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2956 0 0 161 3117
Biso mean---45.31 -
Num. residues----376
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.013022
X-RAY DIFFRACTIONf_angle_d1.3654084
X-RAY DIFFRACTIONf_chiral_restr0.055444
X-RAY DIFFRACTIONf_plane_restr0.007532
X-RAY DIFFRACTIONf_dihedral_angle_d15.9161102
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A1699X-RAY DIFFRACTION10.61TORSIONAL
12B1699X-RAY DIFFRACTION10.61TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 7

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.0836-2.19340.30871300.30733560369096
2.1934-2.33080.32391550.29373575373097
2.3308-2.51080.31011610.27843599376098
2.5108-2.76340.28341370.27273622375998
2.7634-3.16320.29221460.25993625377197
3.1632-3.98510.32731300.21243510364094
3.9851-47.87750.18711530.19113527368093

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