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- PDB-8czn: Crystal Structure of EcDsbA in a complex with 1H-pyrrole-3-carbox... -

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Basic information

Entry
Database: PDB / ID: 8czn
TitleCrystal Structure of EcDsbA in a complex with 1H-pyrrole-3-carboxylic acid
ComponentsThiol:disulfide interchange protein DsbA
KeywordsOXIDOREDUCTASE / DISULFIDE OXIDOREDUCTASE / REDOX PROTEIN / Microfrag screening / FBDD / Fragment
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
COPPER (II) ION / 1H-pyrrole-3-carboxylic acid / Thiol:disulfide interchange protein DsbA
Similarity search - Component
Biological speciesEscherichia coli K-12 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 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 1.3Oct 16, 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)42,8187
Polymers42,3102
Non-polymers5085
Water6,485360
1
A: Thiol:disulfide interchange protein DsbA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,4884
Polymers21,1551
Non-polymers3333
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)21,3303
Polymers21,1551
Non-polymers1752
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)118.439, 63.190, 75.668
Angle α, β, γ (deg.)90.000, 124.021, 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 3 through 13 or (resid 14...
d_2ens_1(chain "B" and (resid 3 or (resid 4 and (name...

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_11ens_1TYRPHEA1 - 34
d_12ens_1VALASPA37 - 65
d_13ens_1GLYVALA67 - 173
d_14ens_1GLNLYSA175 - 186
d_21ens_1TYRPHEE3 - 36
d_22ens_1VALASPE39 - 67
d_23ens_1GLYVALE69 - 175
d_24ens_1GLNLYSE177 - 188

NCS oper: (Code: givenMatrix: (-0.965607807855, 0.0637850787006, 0.252057582994), (-0.251770538593, 0.0126309586466, -0.967704528655), (-0.0649088384265, -0.997883721993, 0.00386265132877)Vector: 36. ...NCS oper: (Code: given
Matrix: (-0.965607807855, 0.0637850787006, 0.252057582994), (-0.251770538593, 0.0126309586466, -0.967704528655), (-0.0649088384265, -0.997883721993, 0.00386265132877)
Vector: 36.6160135381, 15.3751609091, 22.6121520725)

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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-PKN / 1H-pyrrole-3-carboxylic acid


Mass: 111.099 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C5H5NO2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-CU / COPPER (II) ION


Mass: 63.546 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cu
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 360 / 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: 2.8 Å3/Da / Density % sol: 56.13 %
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: 1.59→48.14 Å / Num. obs: 62171 / % possible obs: 99.1 % / Redundancy: 6.7 % / Biso Wilson estimate: 22.88 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.084 / Rpim(I) all: 0.053 / Rrim(I) all: 0.1 / Χ2: 0.5 / Net I/σ(I): 10.6
Reflection shellResolution: 1.59→1.61 Å / Redundancy: 5.9 % / Rmerge(I) obs: 1.726 / Mean I/σ(I) obs: 0.8 / Num. unique obs: 2545 / CC1/2: 0.369 / Rpim(I) all: 0.821 / Χ2: 0.369 / % possible all: 82.5

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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: 1.7→31.6 Å / SU ML: 0.2367 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 23.3131
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2151 784 1.54 %
Rwork0.1918 50210 -
obs0.1922 50994 99.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 27.34 Å2
Refinement stepCycle: LAST / Resolution: 1.7→31.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2852 0 33 364 3249
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072994
X-RAY DIFFRACTIONf_angle_d0.86954068
X-RAY DIFFRACTIONf_chiral_restr0.0497447
X-RAY DIFFRACTIONf_plane_restr0.0063561
X-RAY DIFFRACTIONf_dihedral_angle_d4.6252429
Refine LS restraints NCSType: Torsion NCS / Rms dev position: 1.0782598151 Å
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.810.31481270.25998363X-RAY DIFFRACTION99.96
1.81-1.950.24511200.21768296X-RAY DIFFRACTION99.91
1.95-2.140.2431320.22058317X-RAY DIFFRACTION99.91
2.14-2.450.2081120.20188387X-RAY DIFFRACTION99.87
2.45-3.090.21151510.19368355X-RAY DIFFRACTION99.93
3.09-31.60.19691420.16838492X-RAY DIFFRACTION99.78
Refinement TLS params.Method: refined / Origin x: 19.9043326833 Å / Origin y: 0.102637454795 Å / Origin z: 14.2727659789 Å
111213212223313233
T0.191879337405 Å2-0.00579801872689 Å2-0.0107499547525 Å2-0.164840887773 Å20.0047120857028 Å2--0.170269910425 Å2
L0.508247774457 °20.282323053033 °2-0.0424277969008 °2-0.534503481633 °20.0890602770448 °2--0.579473019527 °2
S-3.79423379193E-6 Å °0.0460989991035 Å °-0.0162552631187 Å °-0.00183722043158 Å °-0.00713969210744 Å °0.0536838856976 Å °-0.0251790602782 Å °-0.00937669781428 Å °0.00565000327521 Å °
Refinement TLS groupSelection details: all

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