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- PDB-8czm: Crystal Structure of EcDsbA in a complex with 4-bromo-1H-pyrazole -

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Basic information

Entry
Database: PDB / ID: 8czm
TitleCrystal Structure of EcDsbA in a complex with 4-bromo-1H-pyrazole
ComponentsThiol:disulfide interchange protein DsbA
KeywordsOXIDOREDUCTASE / DISULFIDE OXIDOREDUCTASE / REDOX PROTEIN / Microfrag screening / FBDD / Fragment / ANTIMICROBIAL PROTEIN
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 / Thioredoxin-like superfamily
Similarity search - Domain/homology
4-bromo-1H-pyrazole / TRIETHYLENE GLYCOL / Thiol:disulfide interchange protein DsbA
Similarity search - Component
Biological speciesEscherichia coli K-12 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsWhitehouse, R.L. / Ilyichova, O.V. / Taylor, A.J.
Funding support Australia, 2items
OrganizationGrant numberCountry
Australian Research Council (ARC)IC180100021 Australia
Australian Research Council (ARC)DP200100796 Australia
CitationJournal: Rsc Med Chem / Year: 2023
Title: Fragment screening libraries for the identification of protein hot spots and their minimal binding pharmacophores.
Authors: Whitehouse, R.L. / Alwan, W.S. / Ilyichova, O.V. / Taylor, A.J. / Chandrashekaran, I.R. / Mohanty, B. / Doak, B.C. / Scanlon, M.J.
History
DepositionMay 25, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 7, 2022Provider: repository / Type: Initial release
Revision 1.1Feb 22, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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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)43,3429
Polymers42,3102
Non-polymers1,0327
Water4,306239
1
A: Thiol:disulfide interchange protein DsbA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,7435
Polymers21,1551
Non-polymers5884
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)21,5994
Polymers21,1551
Non-polymers4443
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)116.956, 64.900, 75.009
Angle α, β, γ (deg.)90.000, 125.676, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 1 through 3 or (resid 4...
d_2ens_1(chain "B" and (resid 1 through 6 or (resid 7...

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_11ens_1ALATYRA1 - 34
d_12ens_1PHEPHEA36
d_13ens_1GLUTHRA38 - 57
d_14ens_1TYRVALA59 - 88
d_15ens_1VALLYSA90 - 188
d_16ens_1B5B5B
d_17ens_1B5B5C
d_21ens_1ALATYRF1 - 34
d_22ens_1PHEPHEF36
d_23ens_1GLUTHRF38 - 57
d_24ens_1TYRVALF59 - 88
d_25ens_1VALLYSF90 - 188
d_26ens_1B5B5G
d_27ens_1B5B5H

NCS oper: (Code: givenMatrix: (-0.955451901995, 0.0761287735022, 0.285159732114), (-0.290864958777, -0.0788923982165, -0.953505933521), (-0.0500923021048, -0.993972031472, 0.0975210844954)Vector: 34. ...NCS oper: (Code: given
Matrix: (-0.955451901995, 0.0761287735022, 0.285159732114), (-0.290864958777, -0.0788923982165, -0.953505933521), (-0.0500923021048, -0.993972031472, 0.0975210844954)
Vector: 34.0303197246, 14.7482073775, 19.2691246403)

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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 K-12 (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-BYZ / 4-bromo-1H-pyrazole


Mass: 146.973 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H3BrN2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 239 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 2.73 Å3/Da / Density % sol: 54.99 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 6.1
Details: 11-13 % PEG 8000, 5-7.5% GLYCEROL, 100MM NA CACODYLATE PH6.1, 1MM CuCl2

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.95365 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Sep 24, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95365 Å / Relative weight: 1
ReflectionResolution: 1.75→47.5 Å / Num. obs: 45518 / % possible obs: 98.9 % / Redundancy: 7 % / CC1/2: 0.999 / Rmerge(I) obs: 0.057 / Rpim(I) all: 0.032 / Rrim(I) all: 0.061 / Χ2: 0.53 / Net I/σ(I): 15.5
Reflection shellResolution: 1.75→1.78 Å / Redundancy: 6.3 % / Rmerge(I) obs: 1.357 / Mean I/σ(I) obs: 0.8 / Num. unique obs: 2344 / CC1/2: 0.456 / Rpim(I) all: 0.879 / Χ2: 0.43 / % possible all: 93.1

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Processing

Software
NameVersionClassification
PHENIX1.19_4092refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1FVK

1fvk


Resolution: 1.8→37.41 Å / SU ML: 0.2396 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 22.8731
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2209 962 2.29 %
Rwork0.1971 41096 -
obs0.1976 42058 99.25 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 34.19 Å2
Refinement stepCycle: LAST / Resolution: 1.8→37.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2851 0 46 239 3136
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00842994
X-RAY DIFFRACTIONf_angle_d0.91664060
X-RAY DIFFRACTIONf_chiral_restr0.2055448
X-RAY DIFFRACTIONf_plane_restr0.0071559
X-RAY DIFFRACTIONf_dihedral_angle_d6.4782441
Refine LS restraints NCSType: Torsion NCS / Rms dev position: 2.07654819017 Å
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.890.33041410.28465781X-RAY DIFFRACTION98.78
1.89-2.010.23841410.22385823X-RAY DIFFRACTION98.92
2.01-2.170.22971220.20865838X-RAY DIFFRACTION98.95
2.17-2.390.2421430.20215865X-RAY DIFFRACTION99.49
2.39-2.730.23121370.2085879X-RAY DIFFRACTION99.44
2.73-3.440.21961530.21325893X-RAY DIFFRACTION99.77
3.44-37.410.19671250.17136017X-RAY DIFFRACTION99.39
Refinement TLS params.Method: refined / Origin x: 19.1177972925 Å / Origin y: -0.683934857177 Å / Origin z: 12.5717011598 Å
111213212223313233
T0.238664874762 Å2-0.00284085921083 Å2-0.0127867300659 Å2-0.224535290034 Å2-0.00424856016411 Å2--0.218789163671 Å2
L0.616290071754 °20.270735179385 °20.129411753542 °2-0.57251878443 °20.130932128098 °2--0.440673985852 °2
S-0.0148332850819 Å °-0.00259682688793 Å °0.0253617012725 Å °-0.0479002272565 Å °-0.00417608991849 Å °0.0597974557162 Å °-0.0620344478758 Å °-0.0829384484462 Å °0.0241598044879 Å °
Refinement TLS groupSelection details: all

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