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- PDB-7luh: Burkholderia pseudomallei Disulfide bond forming protein A (DsbA)... -

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Basic information

Entry
Database: PDB / ID: 7luh
TitleBurkholderia pseudomallei Disulfide bond forming protein A (DsbA) liganded with fragment bromophenoxy propanamide
ComponentsThiol:disulfide interchange protein
KeywordsOXIDOREDUCTASE / BpsDsbA / Fragment / cryptic-pocket
Function / homology
Function and homology information


disulfide oxidoreductase activity / 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
(2~{R})-2-(4-bromanylphenoxy)propanamide / Thiol:disulfide interchange protein
Similarity search - Component
Biological speciesBurkholderia pseudomallei (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.84 Å
AuthorsPetit, G.A. / Martin, J.L. / McMahon, R.M.
Funding support Australia, 3items
OrganizationGrant numberCountry
Other privateRamaciotti health investment grant- 2017HIG0094 Australia
National Health and Medical Research Council (NHMRC, Australia)1099151 Australia
National Health and Medical Research Council (NHMRC, Australia)1144046 Australia
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2022
Title: Identification and characterization of two drug-like fragments that bind to the same cryptic binding pocket of Burkholderia pseudomallei DsbA.
Authors: Petit, G.A. / Mohanty, B. / McMahon, R.M. / Nebl, S. / Hilko, D.H. / Wilde, K.L. / Scanlon, M.J. / Martin, J.L. / Halili, M.A.
History
DepositionFeb 22, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 5, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 12, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Oct 18, 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,2662
Polymers22,0221
Non-polymers2441
Water3,711206
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: NMR relaxation study, Weak binding between the protein and the ligand.
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)59.539, 62.941, 69.363
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

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Components

#1: Protein Thiol:disulfide interchange protein


Mass: 22022.115 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: The 3 first amino acids are left over from TEV cleavage scar
Source: (gene. exp.) Burkholderia pseudomallei (strain K96243) (bacteria)
Strain: K96243 / Gene: dsbA, BPSL0381 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q63Y08
#2: Chemical ChemComp-YCS / (2~{R})-2-(4-bromanylphenoxy)propanamide


Mass: 244.085 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H10BrNO2 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 206 / 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: 3.03 Å3/Da / Density % sol: 59.35 % / Description: Long needles, transparent
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 60% Tacsimate Cryo protected in 20% Ethylen Glycol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Nov 22, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.84→46.62 Å / Num. obs: 23090 / % possible obs: 98.75 % / Redundancy: 6.7 % / Biso Wilson estimate: 31.21 Å2 / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.071 / Rpim(I) all: 0.03 / Rrim(I) all: 0.077 / Net I/σ(I): 16
Reflection shellResolution: 1.84→1.91 Å / Redundancy: 2 % / Rmerge(I) obs: 1.27 / Mean I/σ(I) obs: 1.51 / Num. unique obs: 2249 / CC1/2: 0.633 / CC star: 0.88 / Rpim(I) all: 0.512 / Rrim(I) all: 1.37 / % possible all: 98.38

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Processing

Software
NameVersionClassification
PHENIX1.19_4092refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4K2D

4k2d


Resolution: 1.84→46.61 Å / SU ML: 0.2374 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 20.0311
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Details: Cycle of automated refinement with Phenix refine, using geometry and ADP weight optimisation. TLS (3 groups: residues 7-70, 71-137 and 138-197). Occupancy of the ligand was set to 0.5 and ...Details: Cycle of automated refinement with Phenix refine, using geometry and ADP weight optimisation. TLS (3 groups: residues 7-70, 71-137 and 138-197). Occupancy of the ligand was set to 0.5 and then refined using occupancy refinement. Manual refinement using coot V 0.9.5
RfactorNum. reflection% reflectionSelection details
Rfree0.194 1992 8.62 %Random
Rwork0.165 21119 --
obs0.1701 23063 98.71 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 37.15 Å2
Refinement stepCycle: LAST / Resolution: 1.84→46.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1494 0 13 206 1713
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081587
X-RAY DIFFRACTIONf_angle_d0.83742165
X-RAY DIFFRACTIONf_chiral_restr0.0531235
X-RAY DIFFRACTIONf_plane_restr0.0072284
X-RAY DIFFRACTIONf_dihedral_angle_d15.6181584
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.84-1.880.39591160.36891379X-RAY DIFFRACTION90.72
1.88-1.930.3011370.28051475X-RAY DIFFRACTION98.59
1.93-1.990.2751470.22811489X-RAY DIFFRACTION98.85
1.99-2.050.22551380.19561493X-RAY DIFFRACTION98.91
2.05-2.130.22651410.17591497X-RAY DIFFRACTION99.15
2.13-2.210.22141520.17681471X-RAY DIFFRACTION99.33
2.21-2.310.20451360.1731507X-RAY DIFFRACTION99.52
2.31-2.430.2091390.17351503X-RAY DIFFRACTION99.45
2.43-2.590.22671470.16751521X-RAY DIFFRACTION99.52
2.59-2.790.21681420.16361527X-RAY DIFFRACTION99.7
2.79-3.070.22031430.18541519X-RAY DIFFRACTION99.76
3.07-3.510.18251520.1581552X-RAY DIFFRACTION99.82
3.51-4.420.14951460.13551548X-RAY DIFFRACTION99.53
4.42-46.610.1721560.15371638X-RAY DIFFRACTION99.06
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.727844027080.154152243429-0.03430967161414.519751911050.8415811569732.294445838930.02924520184230.16398618451-0.3363276313790.1426449108080.0497592410651-0.08228342853480.233149921504-0.00453667546246-0.07623810348190.204112124533-0.00168211012615-0.03009103957320.258337197568-0.04727030413680.2068698672453.65725777819-24.3385411747-4.96911904385
26.41801351279-0.6199657069950.1972330472353.6880202071.273151945064.45314999141-0.0435102016111-0.2440246913190.7030166595710.005641395646410.01614966186920.0318955674196-0.338294763125-0.1822929452980.02582755980910.2338992609220.0485235508814-0.002307963415690.219499154097-0.02636627631490.274194069973.92690114276-3.032518534230.778351847274
34.193692083792.825188646130.5989406304395.146445998551.674354443881.15333404765-0.03503811269590.379138923817-0.372164542929-0.02074743880240.0686515938999-0.3573483216870.06285197930310.00455981422427-0.01020184049090.2332335998460.0307568617573-0.005479157833670.305877717584-0.04001286709760.230555864747.53326676803-23.7227951756-8.35425920152
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A

IDRefine TLS-IDSelection detailsAuth seq-IDLabel seq-ID
11chain A and (resid 7:70)7 - 701 - 64
22chain A and (resid 71:137)71 - 13765 - 131
33chain A and (resid 138:197)138 - 197132 - 191

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