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- PDB-4zl8: Crystal structure of Pseudomonas aeruginosa DsbA E82I: Crystal II -

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Basic information

Entry
Database: PDB / ID: 4zl8
TitleCrystal structure of Pseudomonas aeruginosa DsbA E82I: Crystal II
ComponentsThiol:disulfide interchange protein DsbA
KeywordsOXIDOREDUCTASE / thioredoxin fold
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 / Glutaredoxin / Glutaredoxin / Thioredoxin-like superfamily ...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
Thiol:disulfide interchange protein DsbA
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.395 Å
AuthorsMcMahoh, R.M. / Martin, J.L.
Funding support Australia, 1items
OrganizationGrant numberCountry
Australian Research Council (ARC)LP0990166 Australia
CitationJournal: Acta Crystallogr. D Biol. Crystallogr. / Year: 2015
Title: Sent packing: protein engineering generates a new crystal form of Pseudomonas aeruginosa DsbA1 with increased catalytic surface accessibility.
Authors: McMahon, R.M. / Coincon, M. / Tay, S. / Heras, B. / Morton, C.J. / Scanlon, M.J. / Martin, J.L.
History
DepositionMay 1, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 9, 2015Provider: repository / Type: Initial release
Revision 1.1Apr 18, 2018Group: Data collection / Database references / Derived calculations
Category: citation / diffrn_source / pdbx_struct_oper_list
Item: _citation.journal_abbrev / _citation.pdbx_database_id_PubMed ..._citation.journal_abbrev / _citation.pdbx_database_id_PubMed / _citation.title / _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Sep 27, 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

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Assembly

Deposited unit
A: Thiol:disulfide interchange protein DsbA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,9156
Polymers21,3521
Non-polymers5645
Water3,693205
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)35.280, 63.680, 41.980
Angle α, β, γ (deg.)90.000, 98.260, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Thiol:disulfide interchange protein DsbA


Mass: 21351.514 Da / Num. of mol.: 1 / Fragment: UNP residues 22-211 / Mutation: E82I
Source method: isolated from a genetically manipulated source
Details: The first three residues (SNA) derive from an expression tag
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Strain: ATCC 15692 / PAO1 / 1C / PRS 101 / LMG 12228 / Gene: dsbA, PA5489 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) pLysS / References: UniProt: P0C2B2
#2: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID / MES (buffer)


Mass: 195.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 205 / 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: 2.24 Å3/Da / Density % sol: 45.09 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6 / Details: 20-29 % PEG 1500, 0.1 M MES

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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: Feb 13, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.395→41.545 Å / Num. all: 36539 / Num. obs: 36539 / % possible obs: 99.8 % / Redundancy: 3.6 % / Rsym value: 0.08 / Net I/σ(I): 9.7
Reflection shellResolution: 1.395→1.47 Å / Redundancy: 3.5 % / Mean I/σ(I) obs: 3.2 / % possible all: 99.9

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation1.44 Å34.91 Å
Translation1.44 Å34.91 Å

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Processing

Software
NameVersionClassification
PHENIXrefinement
MOSFLMdata reduction
SCALAdata scaling
PHASER2.5.0phasing
PDB_EXTRACT3.15data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3H93

3h93


Resolution: 1.395→34.914 Å / FOM work R set: 0.9074 / SU ML: 0.09 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 16.06 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1594 1838 5.03 %
Rwork0.146 34677 -
obs0.1467 36515 99.78 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 68.67 Å2 / Biso mean: 17.32 Å2 / Biso min: 7.8 Å2
Refinement stepCycle: final / Resolution: 1.395→34.914 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1467 0 81 205 1753
Biso mean--24.93 28.74 -
Num. residues----187
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0091574
X-RAY DIFFRACTIONf_angle_d1.2942129
X-RAY DIFFRACTIONf_chiral_restr0.066226
X-RAY DIFFRACTIONf_plane_restr0.007266
X-RAY DIFFRACTIONf_dihedral_angle_d12.675599
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 13 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.395-1.43270.24381390.207226392778
1.4327-1.47490.23311540.185526612815
1.4749-1.52250.19341330.161226572790
1.5225-1.57690.18891290.15426802809
1.5769-1.640.17081250.143226642789
1.64-1.71470.16231590.138926422801
1.7147-1.80510.15631470.13526582805
1.8051-1.91820.1521420.136226622804
1.9182-2.06620.16131400.134626692809
2.0662-2.27410.14341530.130326462799
2.2741-2.60310.14811230.138926852808
2.6031-3.27930.14351540.149226752829
3.2793-34.92490.15221400.149927392879
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)
12.2949-0.009-0.12270.905-0.05190.42020.0098-0.0729-0.1108-0.0307-0.0064-0.02510.02670.0276-0.00290.0940.0022-0.00440.0735-0.00670.0758112.137-12.319440.44
21.62970.60150.73942.98170.62743.35890.0406-0.113-0.0350.2589-0.00980.09790.0671-0.0965-0.01990.07790.00390.01380.08070.01380.0805100.8418-5.226156.0014
30.9817-2.4998-2.16436.36885.51014.76720.15680.12850.0792-0.2108-0.0687-0.0125-0.4644-0.1557-0.03470.1402-0.01160.01980.10370.02090.1143107.50434.606442.9255
44.0735-0.88340.30481.1234-0.14051.07760.03240.129-0.2483-0.0894-0.01280.02790.06050.0017-0.01160.0865-0.0050.00230.0601-0.01410.0774114.8579-15.52234.2572
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 6 through 68 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 69 through 131 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 132 through 148 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 149 through 191 )A0

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