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- PDB-5vyo: The complex structure of Burkholderia pseudomallei DsbA bound to ... -

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Basic information

Entry
Database: PDB / ID: 5vyo
TitleThe complex structure of Burkholderia pseudomallei DsbA bound to a peptide
Components
  • Disulfide bond formation protein B
  • Thiol:disulfide interchange protein
KeywordsOXIDOREDUCTASE / thioredoxin / complex
Function / homology
Function and homology information


disulfide oxidoreductase activity / protein-disulfide reductase activity / protein folding / membrane => GO:0016020 / periplasmic space / electron transfer activity / plasma membrane
Similarity search - Function
Disulphide bond formation protein DsbB/BdbC / Disulphide bond formation protein DsbB / DsbB-like superfamily / Disulfide bond formation protein DsbB / Thiol:disulphide interchange protein DsbA/DsbL / DSBA-like thioredoxin domain / DSBA-like thioredoxin domain / Thioredoxin, conserved site / Thioredoxin family active site. / Thioredoxin domain profile. ...Disulphide bond formation protein DsbB/BdbC / Disulphide bond formation protein DsbB / DsbB-like superfamily / Disulfide bond formation protein DsbB / 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
Disulfide bond formation protein B / Thiol:disulfide interchange protein
Similarity search - Component
Biological speciesBurkholderia pseudomallei (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.49 Å
AuthorsMcMahon, R.M. / Martin, J.L.
Funding support Australia, 1items
OrganizationGrant numberCountry
National Health and Medical Research Council (NHMRC, Australia)1061241 Australia
CitationJournal: Infect. Immun. / Year: 2018
Title: Virulence of the Melioidosis Pathogen Burkholderia pseudomallei Requires the Oxidoreductase Membrane Protein DsbB.
Authors: McMahon, R.M. / Ireland, P.M. / Sarovich, D.S. / Petit, G. / Jenkins, C.H. / Sarkar-Tyson, M. / Currie, B.J. / Martin, J.L.
History
DepositionMay 25, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 21, 2018Provider: repository / Type: Initial release
Revision 1.1Mar 28, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2May 9, 2018Group: Data collection / Database references / Category: citation / Item: _citation.journal_volume / _citation.title
Revision 1.3Jan 8, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Oct 4, 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

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
E: Disulfide bond formation protein B
F: Disulfide bond formation protein B
G: Disulfide bond formation protein B
H: Disulfide bond formation protein B


Theoretical massNumber of molelcules
Total (without water)90,4278
Polymers90,4278
Non-polymers00
Water5,116284
1
A: Thiol:disulfide interchange protein
F: Disulfide bond formation protein B


Theoretical massNumber of molelcules
Total (without water)22,6072
Polymers22,6072
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area890 Å2
ΔGint-10 kcal/mol
Surface area9910 Å2
MethodPISA
2
B: Thiol:disulfide interchange protein
E: Disulfide bond formation protein B


Theoretical massNumber of molelcules
Total (without water)22,6072
Polymers22,6072
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area890 Å2
ΔGint-10 kcal/mol
Surface area9830 Å2
MethodPISA
3
C: Thiol:disulfide interchange protein
G: Disulfide bond formation protein B


Theoretical massNumber of molelcules
Total (without water)22,6072
Polymers22,6072
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area860 Å2
ΔGint-8 kcal/mol
Surface area10180 Å2
MethodPISA
4
D: Thiol:disulfide interchange protein
H: Disulfide bond formation protein B


Theoretical massNumber of molelcules
Total (without water)22,6072
Polymers22,6072
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area900 Å2
ΔGint-10 kcal/mol
Surface area9900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.794, 59.684, 71.759
Angle α, β, γ (deg.)89.490, 67.790, 81.030
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Thiol:disulfide interchange protein / Disulfide Bond Protein A


Mass: 21990.049 Da / Num. of mol.: 4 / Mutation: C46A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Burkholderia pseudomallei (bacteria) / Strain: K96243 / Gene: dsbA, BPSL0381 / Plasmid: pET21a / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) pLysS / References: UniProt: Q63Y08
#2: Protein/peptide
Disulfide bond formation protein B / Disulfide oxidoreductase


Mass: 616.687 Da / Num. of mol.: 4 / Fragment: UNP residues 99-104 / Source method: obtained synthetically / Source: (synth.) Burkholderia pseudomallei (bacteria) / References: UniProt: Q63RY4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 284 / Source method: isolated from a natural source / Formula: H2O

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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: 2.55 Å3/Da / Density % sol: 51.73 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.1 M HEPES, pH 7.0, 0.5% v/v Jeffamine ED-2001, 1.74 M sodium malonate, pH 7.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 18, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.49→58.87 Å / Num. obs: 29113 / % possible obs: 96.6 % / Redundancy: 3.8 % / Biso Wilson estimate: 24.03 Å2 / CC1/2: 0.993 / Rmerge(I) obs: 0.111 / Rpim(I) all: 0.066 / Rrim(I) all: 0.129 / Net I/σ(I): 10.3
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsCC1/2Rpim(I) allRrim(I) all% possible all
2.49-2.623.70.4540.8560.270.52987.7
7.87-58.873.80.040.9980.0240.04797.1

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation4.07 Å42.88 Å
Translation4.07 Å42.88 Å

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
Aimless0.1.27data scaling
PHASER2.6.0phasing
PDB_EXTRACT3.22data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 4K2D

4k2d


Resolution: 2.49→41.309 Å / SU ML: 0.33 / Cross valid method: FREE R-VALUE / σ(F): 1.97 / Phase error: 27.48
RfactorNum. reflection% reflection
Rfree0.255 1472 5.06 %
Rwork0.1971 --
obs0.2001 29095 96.59 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 128.99 Å2 / Biso mean: 34.8368 Å2 / Biso min: 8.34 Å2
Refinement stepCycle: final / Resolution: 2.49→41.309 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6115 0 0 284 6399
Biso mean---27.38 -
Num. residues----781
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0026296
X-RAY DIFFRACTIONf_angle_d0.4878540
X-RAY DIFFRACTIONf_chiral_restr0.042924
X-RAY DIFFRACTIONf_plane_restr0.0041102
X-RAY DIFFRACTIONf_dihedral_angle_d12.2213764
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 11

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.4898-2.57020.33781280.27172089221781
2.5702-2.6620.31631150.24782557267298
2.662-2.76860.2981440.24262553269798
2.7686-2.89460.31041230.22542578270198
2.8946-3.04710.29791340.22542553268798
3.0471-3.2380.29461390.21712565270499
3.238-3.48780.28011340.20352530266498
3.4878-3.83860.22941210.17622559268098
3.8386-4.39350.20851590.15942519267897
4.3935-5.53330.21061540.16022557271199
5.5333-41.31440.21361210.18242563268498
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)
16.3517-0.659-0.17715.39370.21866.01440.47990.8938-0.3096-0.905-0.0179-0.37310.31550.5605-0.11680.29810.09730.06830.3401-0.01940.3006-26.223110.8896-6.7753
23.1612-1.3170.54761.0361-0.51771.44030.02170.1556-0.2514-0.09770.0568-0.3164-0.1856-0.0340.01230.2785-0.0449-0.0160.14740.0070.1927-37.654217.58853.4205
35.5973-1.55231.50524.454-0.10754.2035-0.1002-0.4052-0.06620.44750.1412-0.2335-0.0791-0.0231-0.08980.2583-0.05080.02230.15050.03270.1112-36.416511.784110.9926
44.09760.9575-1.12586.31641.17933.70940.03120.22960.2215-0.39260.06680.1604-0.2317-0.1247-0.12250.18790.0076-0.01280.17150.00810.2169-52.223322.04824.2713
52.90430.6504-1.36736.24230.85743.98990.0486-0.2551-0.0640.218-0.11210.11380.24010.03110.04830.1738-0.0466-0.01060.15150.04860.1722-57.685112.72078.7287
63.75471.1773-1.21467.1107-0.75313.87450.0818-0.57810.26231.1020.0470.9155-0.0502-0.195-0.1360.3535-0.00590.06160.29370.00460.2396-59.819123.042115.7147
74.003-2.657-0.65793.5511.23352.15640.0220.3690.3781-0.3057-0.11850.4824-0.2913-0.0214-0.16370.3363-0.054-0.10640.1323-0.020.3665-45.861930.00764.512
83.1519-0.1535-0.95716.29531.38841.5897-0.0190.26030.1242-0.3706-0.0553-0.0221-0.05520.11540.15650.2661-0.0028-0.01510.1866-0.01290.1383-34.566516.382-2.5791
94.9160.6152-1.02955.67750.31813.40370.19740.0062-0.18640.0466-0.1792-0.98420.28850.49580.04830.17330.0102-0.04860.16390.02420.3383-25.65110.51713.6588
102.27470.0588-1.44234.3419-0.27513.6187-0.16650.0567-0.1988-0.21420.0617-0.1470.16350.11930.12110.2339-0.0229-0.04830.14380.05390.2071-46.71793.5635-26.5721
112.6131-1.2616-1.46745.59380.36494.50270.0913-0.01960.2102-0.2670.09740.1448-0.0193-0.0121-0.17350.1314-0.0446-0.01390.17660.00960.2255-53.665913.049-28.204
123.17581.16780.1995.61760.8052.81310.0408-0.04570.07080.1801-0.00050.3569-0.0292-0.2388-0.03660.14740.03940.01170.14460.00440.1285-67.396510.9181-15.0535
133.09141.0604-1.26162.1187-0.22891.0630.09580.0558-0.31040.0916-0.097-0.17080.21870.07060.09420.19790.0197-0.02140.16440.00220.1594-51.11141.4628-20.93
143.3328-0.2041-2.15252.74910.59923.35260.02430.20610.1193-0.40510.0436-0.52210.1740.0299-0.08420.24260.01410.01530.2003-0.00680.3456-41.84789.1967-34.104
157.236-0.497-1.21028.8917-0.20333.98930.2635-1.0804-0.42710.8660.3040.89430.6988-0.8579-0.19350.4193-0.09730.1110.47040.0680.3129-70.8141-14.405824.3532
164.68010.25960.13323.07741.25711.2037-0.1250.0422-0.02630.25440.04240.22480.085-0.050.1310.2178-0.0413-0.0020.18190.02040.151-55.7682-11.899411.8168
172.91950.1094-0.49276.31920.53742.64250.01650.2893-0.2352-0.3462-0.0051-0.391-0.00080.0316-0.00040.21470.0256-0.01960.16370.0170.1614-36.2416-15.53659.0452
185.17392.5082-3.64451.9216-1.76823.6827-0.0530.02990.46250.2243-0.0667-0.5058-0.6985-0.13580.05060.3545-0.0041-0.03140.20140.02360.2873-42.6314-0.653813.4267
193.36511.28540.58295.172-0.41173.506-0.0457-0.15630.12930.0395-0.09270.4249-0.0944-0.14170.13550.19940.0090.05070.2173-0.06550.2076-62.3188-11.518417.3739
202.0664-1.46270.38331.9247-2.98439.1914-0.0668-0.32030.26170.0578-0.47440.1097-0.2041-0.55670.72690.176-0.0645-0.01540.3396-0.11250.5807-86.6214-16.2485-22.2652
212.2654-0.2302-1.61884.96770.59962.1345-0.0417-0.02880.05090.21310.00840.2347-0.07810.02640.00090.20020.0238-0.04450.15990.0090.1482-69.6646-19.3702-21.1123
221.2557-0.3293-0.316.0347-2.63251.36690.00390.0995-0.05080.1205-0.0747-0.2422-0.21070.27230.14320.2444-0.0143-0.00440.1730.02850.1738-58.981-21.0941-31.6469
234.9529-0.39440.87118.3454-1.97573.4918-0.0363-0.01020.4982-0.0577-0.2584-0.2632-0.07610.29830.13330.2165-0.0559-0.02810.1698-0.01680.1749-51.8376-17.2069-37.2681
241.94820.1870.7228.64890.46744.13230.3620.019-0.4740.0721-0.0608-1.65320.02740.55890.16480.24570.037-0.05720.27650.06940.3255-47.6714-28.1898-31.5906
253.5942-4.4587-2.12696.62520.83834.1806-0.5586-0.1038-0.0308-0.32040.4625-0.11210.3773-0.20820.05130.2611-0.017-0.0330.18730.02850.2147-65.9894-33.4401-30.1696
263.1423-0.34420.87518.3647-0.83374.6627-0.03550.0642-0.1775-0.1174-0.1077-0.0881-0.1451-0.29240.08250.18450.01770.06720.1712-0.00910.2439-76.7422-23.2096-25.3762
273.7343-0.0519-0.24087.3039-0.43893.44960.0655-0.23860.34050.64040.10910.5851-0.3338-0.33090.00960.23180.0450.02010.2597-0.05980.27-80.023-15.0272-18.2709
287.5049-1.1886-2.37523.24490.31171.7095-0.11520.0014-0.610.1376-0.6941.21030.5342-0.66940.44090.5682-0.1222-0.05820.3468-0.17390.4828-46.332610.5137-12.1092
293.9905-2.0133-3.10643.234-2.71092.00060.4334-0.28960.50430.5622-0.29160.3694-1.1325-0.8260.46970.5927-0.0987-0.06220.4941-0.10430.4858-44.555612.9561-8.2799
306.07926.16630.38311.99974.24213.7604-0.8112-0.22030.6291-0.30710.5979-1.2502-1.35110.82860.52180.84390.0555-0.22170.539-0.04050.5348-49.7001-15.404126.3972
312.09650.21650.10482.1431.74281.63820.28660.1316-0.38340.5406-0.2511-0.61120.61880.64540.10720.68330.1716-0.14740.52960.19430.5118-74.9995-15.4224-36.3584
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 9 through 18 )A9 - 18
2X-RAY DIFFRACTION2chain 'A' and (resid 19 through 49 )A19 - 49
3X-RAY DIFFRACTION3chain 'A' and (resid 50 through 70 )A50 - 70
4X-RAY DIFFRACTION4chain 'A' and (resid 71 through 90 )A71 - 90
5X-RAY DIFFRACTION5chain 'A' and (resid 91 through 123 )A91 - 123
6X-RAY DIFFRACTION6chain 'A' and (resid 124 through 137 )A124 - 137
7X-RAY DIFFRACTION7chain 'A' and (resid 138 through 153 )A138 - 153
8X-RAY DIFFRACTION8chain 'A' and (resid 154 through 177 )A154 - 177
9X-RAY DIFFRACTION9chain 'A' and (resid 178 through 197 )A178 - 197
10X-RAY DIFFRACTION10chain 'B' and (resid 9 through 43 )B9 - 43
11X-RAY DIFFRACTION11chain 'B' and (resid 44 through 70 )B44 - 70
12X-RAY DIFFRACTION12chain 'B' and (resid 71 through 137 )B71 - 137
13X-RAY DIFFRACTION13chain 'B' and (resid 138 through 177 )B138 - 177
14X-RAY DIFFRACTION14chain 'B' and (resid 178 through 197 )B178 - 197
15X-RAY DIFFRACTION15chain 'C' and (resid 7 through 16 )C7 - 16
16X-RAY DIFFRACTION16chain 'C' and (resid 17 through 70 )C17 - 70
17X-RAY DIFFRACTION17chain 'C' and (resid 71 through 137 )C71 - 137
18X-RAY DIFFRACTION18chain 'C' and (resid 138 through 153 )C138 - 153
19X-RAY DIFFRACTION19chain 'C' and (resid 154 through 197 )C154 - 197
20X-RAY DIFFRACTION20chain 'D' and (resid 10 through 19 )D10 - 19
21X-RAY DIFFRACTION21chain 'D' and (resid 20 through 70 )D20 - 70
22X-RAY DIFFRACTION22chain 'D' and (resid 71 through 105 )D71 - 105
23X-RAY DIFFRACTION23chain 'D' and (resid 106 through 124 )D106 - 124
24X-RAY DIFFRACTION24chain 'D' and (resid 125 through 137 )D125 - 137
25X-RAY DIFFRACTION25chain 'D' and (resid 138 through 153 )D138 - 153
26X-RAY DIFFRACTION26chain 'D' and (resid 154 through 167 )D154 - 167
27X-RAY DIFFRACTION27chain 'D' and (resid 168 through 197 )D168 - 197
28X-RAY DIFFRACTION28chain 'E' and (resid 99 through 104 )E99 - 104
29X-RAY DIFFRACTION29chain 'F' and (resid 99 through 104 )F99 - 104
30X-RAY DIFFRACTION30chain 'G' and (resid 99 through 104 )G99 - 104
31X-RAY DIFFRACTION31chain 'H' and (resid 99 through 104 )H99 - 104

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