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- PDB-5hfg: Cytosolic disulfide reductase DsbM from Pseudomonas aeruginosa -

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Basic information

Entry
Database: PDB / ID: 5hfg
TitleCytosolic disulfide reductase DsbM from Pseudomonas aeruginosa
ComponentsUncharacterized protein, cytosolic disulfide reductase DsbM
KeywordsOXIDOREDUCTASE / Dsb / DsbM / disulfide reductase / thioredoxin superfamlily
Function / homologyDSBA-like thioredoxin domain / DSBA-like thioredoxin domain / Glutaredoxin / Glutaredoxin / Thioredoxin-like superfamily / oxidoreductase activity / 3-Layer(aba) Sandwich / Alpha Beta / DSBA-like thioredoxin domain-containing protein
Function and homology information
Biological speciesPseudomonas aeruginosa PAO1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.823 Å
AuthorsJo, I. / Ha, N.-C.
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2016
Title: Crystal structures of the disulfide reductase DsbM from Pseudomonas aeruginosa
Authors: Jo, I. / Park, N. / Chung, I.Y. / Cho, Y.H. / Ha, N.-C.
History
DepositionJan 7, 2016Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 26, 2016Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Uncharacterized protein, cytosolic disulfide reductase DsbM


Theoretical massNumber of molelcules
Total (without water)25,2871
Polymers25,2871
Non-polymers00
Water1,72996
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area9750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)38.808, 38.808, 233.482
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11A-383-

HOH

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Components

#1: Protein Uncharacterized protein, cytosolic disulfide reductase DsbM


Mass: 25286.771 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa PAO1 (bacteria) / Strain: PAO1 / Gene: PA0058 / Plasmid: pProEx Hta / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q9I774
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 96 / 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: 1.74 Å3/Da / Density % sol: 29.24 %
Crystal growTemperature: 287 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1M Bis Tris-HCl (pH 6.5), 1% (vol/vol) Tacsimate (Hampton), 2mM Tris(2-carboxyethyl)phosphine, 20% (wt/vol) PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.97933 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Mar 13, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97933 Å / Relative weight: 1
ReflectionResolution: 1.82→50 Å / Num. obs: 17164 / % possible obs: 99.1 % / Redundancy: 16.8 % / Rmerge(I) obs: 0.076 / Net I/σ(I): 32.8
Reflection shellResolution: 1.82→1.85 Å / Redundancy: 8.4 % / Mean I/σ(I) obs: 4.5 / % possible all: 97.7

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
DENZOdata reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2IN3

2in3


Resolution: 1.823→19.992 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.5 / Phase error: 17.63 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2246 840 4.98 %
Rwork0.1835 --
obs0.1855 16872 98.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.823→19.992 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1569 0 0 96 1665
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061622
X-RAY DIFFRACTIONf_angle_d0.8742202
X-RAY DIFFRACTIONf_dihedral_angle_d18.628962
X-RAY DIFFRACTIONf_chiral_restr0.049238
X-RAY DIFFRACTIONf_plane_restr0.005293
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8227-1.93680.28131460.22732509X-RAY DIFFRACTION96
1.9368-2.08620.25121270.20372607X-RAY DIFFRACTION100
2.0862-2.29580.25151440.18742659X-RAY DIFFRACTION100
2.2958-2.62740.25041170.18462673X-RAY DIFFRACTION100
2.6274-3.30780.22021550.18292709X-RAY DIFFRACTION100
3.3078-19.99330.19071510.16692875X-RAY DIFFRACTION98
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)
12.0735-0.2989-0.40661.82960.8421.4699-0.1358-0.033-0.10440.01060.02270.08660.1397-0.05690.13670.2147-0.02490.01060.062-0.01730.1024-9.29188.629715.6896
21.7193-1.06530.33381.9333-1.63251.873-0.0816-0.05110.17070.0167-0.0335-0.3278-0.17930.34280.04640.1743-0.0623-0.02020.0756-0.00790.1565-0.15289.590319.982
33.6814-2.4959-2.28564.16460.79274.42970.35250.3209-0.08170.024-0.31470.9886-0.1119-1.362-0.06420.30160.05850.01680.4581-0.06350.5545-21.037313.10325.8722
48.6062-2.42875.5391.289-0.94014.2160.23340.4504-0.1348-0.62290.2051.3530.7547-0.5701-0.47640.4018-0.1684-0.14370.38470.11680.5114-24.496410.223620.2101
55.5097-2.2733.34243.861-2.00745.8731-0.01040.23640.1422-0.09820.1090.543-0.1093-0.7727-0.0320.1120.01420.01510.26550.01180.2518-24.23721.176817.7417
62.0171.58551.10994.20730.07194.23680.070.0231-0.308-0.26940.0887-0.08180.2285-0.0092-0.11830.16850.0075-0.00640.05060.00170.068-6.961318.83737.4906
72.0363-0.9383-0.97852.14160.27261.06820.1066-0.1803-0.0329-0.1463-0.06160.02170.0881-0.0459-0.00670.1629-0.0242-0.01170.08390.0020.0897-9.238919.595816.631
82.30292.3131-1.2812.3524-1.32163.26710.13820.12930.5519-0.1689-0.01240.2606-0.2731-0.3713-0.05770.1850.05090.01020.06660.00380.1747-12.732627.029411.4629
90.2757-0.6049-0.53891.4710.61383.19630.21710.04760.1783-0.4070.0445-0.3385-0.19350.18080.03420.3295-0.02570.09570.06590.01320.1682-1.982326.10335.2313
100.66970.22590.14653.65070.0520.65490.09890.0764-0.1085-0.4760.0702-0.10820.19460.06410.28980.36110.0091-0.00050.0207-0.09290.1363-5.36056.18891.7373
112.92410.82240.76244.7044-0.24525.35440.15450.1446-0.5618-0.0284-0.2455-0.29480.46070.519-0.1270.29060.02150.04570.0092-0.04940.1823-2.365-1.707314.4212
121.9265-0.74930.6393.41791.34651.02540.0696-0.1769-0.29780.3250.07430.29040.3234-0.1544-0.03880.2491-0.02830.05960.05730.02260.2275-9.45590.963825.763
133.8742-3.923-1.49754.01411.11425.09180.0167-0.09140.210.21670.0336-0.4870.23360.4925-0.00330.1832-0.0226-0.00730.13720.01030.15661.34081.715128.3935
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 4 through 20 )
2X-RAY DIFFRACTION2chain 'A' and (resid 21 through 39 )
3X-RAY DIFFRACTION3chain 'A' and (resid 40 through 55 )
4X-RAY DIFFRACTION4chain 'A' and (resid 56 through 70 )
5X-RAY DIFFRACTION5chain 'A' and (resid 71 through 88 )
6X-RAY DIFFRACTION6chain 'A' and (resid 89 through 106 )
7X-RAY DIFFRACTION7chain 'A' and (resid 107 through 121 )
8X-RAY DIFFRACTION8chain 'A' and (resid 122 through 139 )
9X-RAY DIFFRACTION9chain 'A' and (resid 140 through 155 )
10X-RAY DIFFRACTION10chain 'A' and (resid 156 through 171 )
11X-RAY DIFFRACTION11chain 'A' and (resid 172 through 190 )
12X-RAY DIFFRACTION12chain 'A' and (resid 191 through 199 )
13X-RAY DIFFRACTION13chain 'A' and (resid 200 through 214 )

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