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

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Basic information

Entry
Database: PDB / ID: 7luj
TitleBurkholderia pseudomallei Disulfide bond forming protein A (DsbA) liganded with fragment 4-methoxy-N-phenylbenzenesulfonamide
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
4-methoxy-~{N}-phenyl-benzenesulfonamide / Thiol:disulfide interchange protein
Similarity search - Component
Biological speciesBurkholderia pseudomallei (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.31 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Thiol:disulfide interchange protein
B: Thiol:disulfide interchange protein
C: Thiol:disulfide interchange protein
D: Thiol:disulfide interchange protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,7117
Polymers88,0884
Non-polymers6233
Water4,197233
1
A: Thiol:disulfide interchange protein


  • defined by author
  • Evidence: NMR relaxation study, Only 2 ligands bind the four protein chains across two different binding site on the protein surface. The first binding site present on chain A, B and D is found near ...Evidence: NMR relaxation study, Only 2 ligands bind the four protein chains across two different binding site on the protein surface. The first binding site present on chain A, B and D is found near Y110. The second binding site is only visible on chain C and found close to C43 in the active site
  • 22 kDa, 1 polymers
  • Search similar-shape structures of this assembly by Omokage search (details)
Theoretical massNumber of molelcules
Total (without water)22,0221
Polymers22,0221
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Thiol:disulfide interchange protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,2852
Polymers22,0221
Non-polymers2631
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Thiol:disulfide interchange protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,1182
Polymers22,0221
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Thiol:disulfide interchange protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,2852
Polymers22,0221
Non-polymers2631
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)69.380, 59.446, 105.427
Angle α, β, γ (deg.)90.000, 104.862, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 10 through 11 or (resid 12...
d_2ens_1(chain "B" and (resid 10 through 11 or (resid 12...
d_3ens_1(chain "C" and (resid 10 through 42 or resid 44...
d_4ens_1(chain "D" and (resid 10 through 11 or (resid 12...

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_11ens_1ALAGLYA2 - 34
d_12ens_1PROPROA36
d_13ens_1TYRILEA39 - 45
d_14ens_1ALAPHEA47 - 65
d_15ens_1ASPTYRA67 - 146
d_16ens_1ILETHRA148 - 167
d_17ens_1SERLEUA169 - 189
d_21ens_1ALAGLYB1 - 33
d_22ens_1PROPROB35
d_23ens_1TYRILEB38 - 44
d_24ens_1ALAPHEB46 - 64
d_25ens_1ASPTYRB66 - 145
d_26ens_1ILETHRB147 - 166
d_27ens_1SERLEUB168 - 188
d_31ens_1ALAGLYC1 - 33
d_32ens_1PROPROC35
d_33ens_1TYRILEC38 - 44
d_34ens_1ALAPHEC46 - 64
d_35ens_1ASPTYRC66 - 145
d_36ens_1ILETHRC147 - 166
d_37ens_1SERLEUC168 - 188
d_41ens_1ALAGLYD4 - 36
d_42ens_1PROPROD38
d_43ens_1TYRILED41 - 47
d_44ens_1ALAPHED49 - 67
d_45ens_1ASPTYRD69 - 148
d_46ens_1ILETHRD150 - 169
d_47ens_1SERLEUD171 - 191

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Components

#1: Protein
Thiol:disulfide interchange protein


Mass: 22022.115 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: The 3 first amino acids are leftover from TEV 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-YCY / 4-methoxy-~{N}-phenyl-benzenesulfonamide


Mass: 263.312 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C13H13NO3S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 233 / 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: 2.45 Å3/Da / Density % sol: 51 % / Description: Long needles
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1M HEPES pH 7.5 0.2M Li2SO4 29.5% PEG3350 Large excess of 4-methoxy-N-phenylbenzenesulfonamide Protein concentrated to 33 mgml-1

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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 16M / Detector: PIXEL / Date: Aug 6, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.31→46.75 Å / Num. obs: 36537 / % possible obs: 97.1 % / Redundancy: 6.6 % / Biso Wilson estimate: 45.07 Å2 / CC1/2: 0.994 / CC star: 0.999 / Rmerge(I) obs: 0.1723 / Rpim(I) all: 0.0722 / Rrim(I) all: 0.1871 / Χ2: 0.48 / Net I/σ(I): 6.88
Reflection shellResolution: 2.31→2.37 Å / Redundancy: 5.5 % / Rmerge(I) obs: 1.358 / Mean I/σ(I) obs: 1.05 / Num. unique obs: 2835 / CC1/2: 0.573 / CC star: 0.854 / Rpim(I) all: 0.5915 / Rrim(I) all: 1.485 / Χ2: 0.25 / % possible all: 77.9

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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: 2.31→46.75 Å / SU ML: 0.339 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 27.5596
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Details: Refinement conducted by alternating between automated refinement cycles with Phenix and manually with coot. Phenix reinfement was conducted using geometry and ADP weight optimisation, TLS (3 ...Details: Refinement conducted by alternating between automated refinement cycles with Phenix and manually with coot. Phenix reinfement was conducted using geometry and ADP weight optimisation, TLS (3 groups per chain, residues N-term-70, 71-137,138-197); ligand occupancy was also set to 0.5 and occupancy refinement was used to find the optimal occupancy.
RfactorNum. reflection% reflectionSelection details
Rfree0.2599 1785 5.01 %RANDOM
Rwork0.2276 33868 --
obs0.2263 35652 97.42 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 60.72 Å2
Refinement stepCycle: LAST / Resolution: 2.31→46.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5844 0 41 233 6118
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0046172
X-RAY DIFFRACTIONf_angle_d0.58658431
X-RAY DIFFRACTIONf_chiral_restr0.044916
X-RAY DIFFRACTIONf_plane_restr0.0041107
X-RAY DIFFRACTIONf_dihedral_angle_d14.4162195
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2AX-RAY DIFFRACTIONTorsion NCS0.443154685124
ens_1d_3AX-RAY DIFFRACTIONTorsion NCS0.552648365674
ens_1d_4AX-RAY DIFFRACTIONTorsion NCS0.508730706127
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.31-2.380.35671020.33382149X-RAY DIFFRACTION80.42
2.38-2.450.32331270.29712575X-RAY DIFFRACTION97.47
2.45-2.520.30771350.29332610X-RAY DIFFRACTION98
2.52-2.610.31461480.2882612X-RAY DIFFRACTION98.64
2.61-2.720.32771590.28482590X-RAY DIFFRACTION98.81
2.72-2.840.28281430.27032653X-RAY DIFFRACTION98.87
2.84-2.990.31971170.26352655X-RAY DIFFRACTION99.07
2.99-3.180.27911230.26962656X-RAY DIFFRACTION99.07
3.18-3.430.27251730.23972596X-RAY DIFFRACTION98.86
3.43-3.770.23421440.20552656X-RAY DIFFRACTION99.08
3.77-4.320.20351370.18252678X-RAY DIFFRACTION99.33
4.32-5.440.22451170.17462708X-RAY DIFFRACTION99.44
5.44-46.750.22651600.20132730X-RAY DIFFRACTION99.18
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)
12.70666504101-1.405596929850.2856849247675.658836342981.556346273074.548157103960.1645322841980.1678921093120.144843092308-0.605841939309-0.206614692631-0.0319974417262-0.0276946273858-0.2979685399180.0187033109020.3296693867340.003507033882820.0006054516337470.3316709220530.03891297884770.335575780365-11.8157564299-3.6767726414741.8160470015
22.990853992830.00660642624184-1.489892260717.955985422451.758945130622.866386512140.228963373209-0.278701581403-0.02117804822760.557506490662-0.1957337742640.1429348479990.164261146899-0.242029052814-0.008800299912170.297616187625-0.119100578944-0.01667461077680.378325830652-0.02031665435210.321098939384-8.71646563668-3.8790047885162.453666564
32.00772816314-0.862386874246-0.2725970316783.20347493884-0.1184105169995.634447935850.1311252270560.28534044681-0.0490462323626-0.696947943531-0.07781798437440.09562461101440.03317682592340.214797745785-0.06813961535020.4003690802750.0522582867659-0.03294080450980.340329554639-0.01474979923730.31262152267519.82750835284.6352360508341.9219589921
43.091783462180.5218828861250.9330681162948.63249753711-0.3592587653875.548247180120.120546376204-0.1559919809080.09451130369650.374987764622-0.157368487397-0.366758904319-0.01157648883680.3618628243070.001340771267890.215714542955-0.041166231358-0.01376023654660.3364761037830.01887506289660.33714017865516.52543200674.7062457450662.412617202
50.742907394437-0.387095083412-0.59661795613.687671937553.167132892675.620619459180.115506116580.17626099932-0.0901500720738-0.483196637019-0.1605669485460.330912569562-0.285798565869-0.1934247459330.0150148202980.371416635440.0304437589126-0.1175914571980.3478017889610.02621914971160.38344557002716.74436597027.9331632115239.9780153089
62.697419737971.433788047290.5176288654349.38969578814-0.03870731621795.9922584762-0.0285964304315-0.41330163595-0.1532713407820.542806690828-0.00749891583065-0.279928882304-0.3125042856890.4546629709210.05944190694080.4330694324050.0278300245033-0.02482953751590.437014970330.00331570778370.3571949019694.66409180547-11.32264928997.52143707473
75.753750388630.239685349164-0.006388314636558.887783143860.8462408749945.39585040916-0.0623979334330.478679578762-0.526571162129-1.34203301633-0.1229607463710.356919370261-0.03330122664530.1357679671510.1899909733890.617965927521-0.002736589642820.01053695393110.436778224865-0.0757267503550.389391698798-0.432724545658-11.5131241801-12.5993106846
81.15275251264-0.6540502152330.2852047031637.57164942474-3.352162060275.443124706420.215666631467-0.1215447457020.00731921173220.895182876722-0.178150907941-0.775618550849-0.5169764288160.69042545408-0.04279610035950.478677572069-0.109381889193-0.07888017465310.43675113123-0.05584931974570.5215042880798.17123306891-7.985897284138.15478543226
94.692681327911.869507092442.48660374024.75743544661.359730668026.798933901610.1145363568-0.115088917222-0.09428727149150.4137149358420.0427075110839-0.3438121915960.2402203123340.488842747607-0.1022681545440.4472232990970.04629572143260.05503880546790.436490167176-0.02956434207380.402464490736.5274764022-22.44419088059.55172731629
102.687521904430.2101505359910.8295096457445.04079982002-0.5944284936775.413957202530.2514522742980.350107247370.0359193193948-0.854118405599-0.4403717192510.591774189337-0.302634458686-0.3356890477350.2217669120260.5637212324010.16916212916-0.005841514494150.588831883679-0.03759282901130.62959418972226.5352142042-22.7691752696-9.59147686724
111.416265270490.9696889864560.08883874793895.85535063196-3.295092347175.840732795280.2451780377340.126609702828-0.0207915101313-0.465047716959-0.2536695046130.09170046196340.180541740626-0.0182133414189-0.01177499626510.3521032081820.07939343105960.04884662105510.302668139798-0.02851587240140.30697761819-9.07515253687-7.4862371147640.0970603426
122.94666205951.22076365712.223831874226.84146989193.837539573514.036821111560.380298989448-0.190486993861-0.0971410262340.749080088764-0.282346835299-0.03544072861990.2458085143360.000159968822863-0.09389652386050.473519921578-0.04791182285870.0718174616630.4311357851510.0607743889950.36700067217434.262225834-25.953201248111.7876618171
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 9 through 70 )AA9 - 701 - 62
22chain 'A' and (resid 71 through 137 )AA71 - 13763 - 129
33chain 'B' and (resid 10 through 70 )BB10 - 701 - 61
44chain 'B' and (resid 71 through 137)BB71 - 13762 - 128
55chain 'B' and (resid 138 through 197 )BB138 - 197129 - 188
66chain 'C' and (resid 10 through 70 )CC10 - 701 - 61
77chain 'C' and (resid 71 through 137 )CC71 - 13762 - 128
88chain 'C' and (resid 138 through 197 )CC138 - 197129 - 188
99chain 'D' and (resid 7 through 70 )DD7 - 701 - 64
1010chain 'D' and (resid 71 through 137 )DD71 - 13765 - 131
1111chain 'A' and (resid 138:197)AA138 - 197130 - 189
1212chain 'D' and (resid 138:197)DD138 - 197132 - 191

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