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- PDB-6pc9: Crystal Structure of EcDsbA in a complex with purified methylpipe... -

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Basic information

Entry
Database: PDB / ID: 6pc9
TitleCrystal Structure of EcDsbA in a complex with purified methylpiperazinone 6
ComponentsThiol:disulfide interchange protein DsbA
KeywordsOXIDOREDUCTASE/OXIDOREDUCTASE INHIBITOR / DISULFIDE OXIDOREDUCTASE / REDOX PROTEIN / OXIDOREDUCTASE-INHIBITOR COMPLEX / REFiLX / OXIDOREDUCTASE / OXIDOREDUCTASE-OXIDOREDUCTASE INHIBITOR complex
Function / homology
Function and homology information


cellular response to antibiotic / protein disulfide isomerase activity / protein-disulfide reductase activity / outer membrane-bounded periplasmic space
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
Chem-O7P / TRIETHYLENE GLYCOL / Thiol:disulfide interchange protein DsbA
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsIlyichova, O.V. / Bentley, M. / Doak, B. / Scanlon, M.J.
Funding support Australia, 2items
OrganizationGrant numberCountry
National Health and Medical Research Council (NHMRC, Australia)Project Grant APP1099151 Australia
Australian Research Council (ARC)LIEF LE160100047 Australia
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
DepositionJun 17, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 20, 2020Provider: repository / Type: Initial release
Revision 1.1Jun 24, 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 / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.name
Revision 1.3Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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 DsbA
B: Thiol:disulfide interchange protein DsbA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,8244
Polymers42,3102
Non-polymers5142
Water1,56787
1
A: Thiol:disulfide interchange protein DsbA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,5182
Polymers21,1551
Non-polymers3631
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Thiol:disulfide interchange protein DsbA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,3052
Polymers21,1551
Non-polymers1501
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)60.534, 76.711, 86.205
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 2 through 13 or (resid 14...
d_2ens_1(chain "B" and (resid 2 through 54 or (resid 55...

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_11ens_1GLNALAA1 - 135
d_12ens_1GLNLYSA138 - 188
d_21ens_1GLNALAC2 - 136
d_22ens_1GLNLYSC138 - 188

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Components

#1: Protein Thiol:disulfide interchange protein DsbA


Mass: 21155.025 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria)
Strain: K12 / Gene: dsbA, dsf, ppfA, b3860, JW3832 / Plasmid: B0013 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P0AEG4
#2: Chemical ChemComp-O7P / 2-methyl-4-{4-[2-(4-methyl-3-oxopiperazin-1-yl)-2-oxoethyl]phenoxy}benzonitrile


Mass: 363.410 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H21N3O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C6H14O4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 87 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.38 Å3/Da / Density % sol: 48.4 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / Details: 25-35 % PEG MME 2000, 100-300 mM KBr

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.95373 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 12, 2018
RadiationMonochromator: DOUBLE SI WITH SAGITTALY BENT SECOND CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95373 Å / Relative weight: 1
ReflectionResolution: 2.3→47.52 Å / Num. obs: 18356 / % possible obs: 99.6 % / Redundancy: 13.2 % / Biso Wilson estimate: 44.36 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.086 / Rpim(I) all: 0.035 / Rrim(I) all: 0.093 / Χ2: 1.04 / Net I/σ(I): 18.1
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 12.3 % / Rmerge(I) obs: 0.735 / Num. unique obs: 1730 / CC1/2: 0.891 / Rpim(I) all: 0.306 / Rrim(I) all: 0.797 / Χ2: 0.99 / % possible all: 96.7

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Processing

Software
NameVersionClassification
PHENIX1.18_3845refinement
XDSdata reduction
Aimless1.11.12data scaling
PHASER2.8.2phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1DSB

1dsb


Resolution: 2.3→43.1 Å / SU ML: 0.2637 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 25.7487
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2438 888 4.85 %
Rwork0.1954 17421 -
obs0.1977 18309 99.43 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 49.91 Å2
Refinement stepCycle: LAST / Resolution: 2.3→43.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2861 0 37 87 2985
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00553002
X-RAY DIFFRACTIONf_angle_d0.76314078
X-RAY DIFFRACTIONf_chiral_restr0.048444
X-RAY DIFFRACTIONf_plane_restr0.0049566
X-RAY DIFFRACTIONf_dihedral_angle_d10.7357449
Refine LS restraints NCSType: Torsion NCS / Rms dev position: 0.925537327094 Å
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.450.27481590.23452801X-RAY DIFFRACTION97.72
2.45-2.630.35031390.24112868X-RAY DIFFRACTION99.57
2.63-2.90.27661420.2382865X-RAY DIFFRACTION99.73
2.9-3.320.30931270.23612914X-RAY DIFFRACTION99.87
3.32-4.180.24111630.18192902X-RAY DIFFRACTION99.87
4.18-43.10.19071580.16363071X-RAY DIFFRACTION99.78

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