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- PDB-5hfi: Cytosolic disulfide reductase DsbM from Pseudomonas aeruginosa wi... -

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Basic information

Entry
Database: PDB / ID: 5hfi
TitleCytosolic disulfide reductase DsbM from Pseudomonas aeruginosa with GSH
ComponentsUncharacterized protein, cytosolic disulfide reductase DsbM
KeywordsOXIDOREDUCTASE / Dsb / DsbM / disulfide reductase / thioredoxin superfamlily
Function / homology
Function and homology information


oxidoreductase activity
Similarity search - Function
DSBA-like thioredoxin domain / DSBA-like thioredoxin domain / Glutaredoxin / Glutaredoxin / Thioredoxin-like superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
GLUTATHIONE / DSBA-like thioredoxin domain-containing protein
Similarity search - Component
Biological speciesPseudomonas aeruginosa PAO1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.801 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
Revision 1.2Apr 3, 2024Group: Derived calculations / Category: struct_conn / struct_conn_type
Item: _struct_conn.conn_type_id / _struct_conn.id ..._struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_leaving_atom_flag / _struct_conn_type.id

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,5372
Polymers25,2301
Non-polymers3071
Water2,486138
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area470 Å2
ΔGint-7 kcal/mol
Surface area9890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.199, 39.199, 236.819
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-495-

HOH

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Components

#1: Protein Uncharacterized protein, cytosolic disulfide reductase DsbM


Mass: 25229.719 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: Chemical ChemComp-GSH / GLUTATHIONE / Glutathione


Mass: 307.323 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17N3O6S
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 138 / 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: 1.8 Å3/Da / Density % sol: 31.78 %
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, 5mM GSSG

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.9796 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Jun 2, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9796 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 18406 / % possible obs: 99.8 % / Redundancy: 12.1 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 37
Reflection shellResolution: 1.8→1.83 Å / Redundancy: 7.2 % / Rmerge(I) obs: 0.473 / Mean I/σ(I) obs: 7.2 / % possible all: 99.8

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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: 5HFG

5hfg


Resolution: 1.801→19.735 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.54 / Phase error: 19.12 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2436 1816 10 %
Rwork0.1929 --
obs0.1978 18165 99.54 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.801→19.735 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1542 0 20 138 1700
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0031598
X-RAY DIFFRACTIONf_angle_d0.6952160
X-RAY DIFFRACTIONf_dihedral_angle_d16.229937
X-RAY DIFFRACTIONf_chiral_restr0.038234
X-RAY DIFFRACTIONf_plane_restr0.005287
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8011-1.84970.28841310.24081181X-RAY DIFFRACTION96
1.8497-1.90410.30241350.2281211X-RAY DIFFRACTION100
1.9041-1.96550.2981370.20931236X-RAY DIFFRACTION100
1.9655-2.03570.25881350.1951217X-RAY DIFFRACTION100
2.0357-2.11710.22471360.18631220X-RAY DIFFRACTION100
2.1171-2.21340.21791400.17961255X-RAY DIFFRACTION100
2.2134-2.32990.24561370.17311239X-RAY DIFFRACTION100
2.3299-2.47560.22641390.18951252X-RAY DIFFRACTION100
2.4756-2.66630.25421390.19591247X-RAY DIFFRACTION100
2.6663-2.93390.25641410.19661275X-RAY DIFFRACTION100
2.9339-3.35660.23591420.19551279X-RAY DIFFRACTION100
3.3566-4.22210.22311470.16721316X-RAY DIFFRACTION100
4.2221-19.73610.23891570.20561421X-RAY DIFFRACTION99
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)
12.6361-1.3825-0.44963.0153-0.08072.9569-0.0023-0.0542-0.05570.12790.0593-0.21840.05270.2781-0.02890.1909-0.0309-0.05350.02220.01310.1145-4.488810.015918.0894
26.3163-2.9754-1.8272.9649-1.76264.65410.98990.33380.1588-0.4768-0.16371.75730.4483-0.9592-0.11720.3743-0.09460.0190.6066-0.07280.9318-24.322814.37948.8844
34.5693-1.44850.75615.1348-1.03954.5868-0.0034-0.3413-0.82280.72520.50682.05540.4197-0.9816-0.07780.1733-0.1247-0.01660.25620.08630.2939-21.80415.018723.6357
45.3714-0.7113-1.4922.30560.47973.41830.0822-0.612-0.0051-0.3983-0.06810.16250.0073-0.5432-0.04690.0683-0.0092-0.10550.1661-0.00120.1018-14.05321.31299.5044
57.5866-1.7178-1.62432.53-0.1481.99650.0729-0.3360.0137-0.0407-0.0179-0.07050.1103-0.0371-0.08710.1089-0.029-0.02780.0674-0.00230.0715-9.246420.643717.0174
63.65942.6089-3.28953.2012-1.31723.91480.09450.15150.36850.07460.10230.1203-0.3942-0.4772-0.04540.11090.0042-0.02760.06290.00460.1368-12.701328.135211.7545
71.4902-1.3657-0.24623.29232.46348.01760.13150.17240.2625-0.27410.6954-1.0905-0.25180.8037-0.21880.2129-0.0471-0.02120.07690.0480.2012-1.900727.15685.5717
83.42270.4719-1.17012.2023-1.32771.34490.36860.558-0.3304-0.9916-0.476-0.38370.1976-0.34660.07030.2653-0.0343-0.03450.0471-0.01040.1454-5.0957.01691.9984
94.51690.6901-1.4673.37012.49684.2724-0.1567-0.4846-0.31730.03610.1167-0.0410.54550.307-0.08660.2456-0.02-0.07240.0510.00360.1809-3.899-0.518715.5657
106.6731-1.3984-0.14373.59430.49634.59930.1613-0.2584-0.12990.15720.0407-0.11070.26930.4034-0.11770.275-0.0221-0.05020.09720.02510.1446-2.55992.811628.3926
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 4 through 39 )
2X-RAY DIFFRACTION2chain 'A' and (resid 40 through 60 )
3X-RAY DIFFRACTION3chain 'A' and (resid 61 through 79 )
4X-RAY DIFFRACTION4chain 'A' and (resid 80 through 106 )
5X-RAY DIFFRACTION5chain 'A' and (resid 107 through 121 )
6X-RAY DIFFRACTION6chain 'A' and (resid 122 through 139 )
7X-RAY DIFFRACTION7chain 'A' and (resid 140 through 155 )
8X-RAY DIFFRACTION8chain 'A' and (resid 156 through 171 )
9X-RAY DIFFRACTION9chain 'A' and (resid 172 through 192 )
10X-RAY DIFFRACTION10chain 'A' and (resid 193 through 213 )

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