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- PDB-4n30: Crystal structure of Pseudomonas aeruginosa DsbA2 -

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Basic information

Entry
Database: PDB / ID: 4n30
TitleCrystal structure of Pseudomonas aeruginosa DsbA2
ComponentsProtein disulfide isomerase
KeywordsOXIDOREDUCTASE / Thioredoxin fold
Function / homology
Function and homology information


Thioredoxin / Thioredoxin-like fold / Thioredoxin domain profile. / Thioredoxin domain / Glutaredoxin / Glutaredoxin / Thioredoxin-like superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SAD / Resolution: 1.3 Å
AuthorsTamu, V.D. / Wahni, K. / Messens, J.
CitationJournal: MBio / Year: 2013
Title: Dissecting the machinery that introduces disulfide bonds in Pseudomonas aeruginosa.
Authors: Arts, I.S. / Ball, G. / Leverrier, P. / Garvis, S. / Nicolaes, V. / Vertommen, D. / Ize, B. / Tamu Dufe, V. / Messens, J. / Voulhoux, R. / Collet, J.F.
History
DepositionOct 6, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 4, 2013Provider: repository / Type: Initial release
Revision 1.1Jan 8, 2014Group: Database references
Revision 1.2Oct 16, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Protein disulfide isomerase


Theoretical massNumber of molelcules
Total (without water)24,0921
Polymers24,0921
Non-polymers00
Water2,450136
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)47.797, 59.380, 59.553
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Protein disulfide isomerase


Mass: 24091.699 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Gene: dsbG, EXA31, RL020 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q7WY37
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 136 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

CrystalDensity Matthews: 1.75 Å3/Da / Density % sol: 29.87 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 0.1mM Bis-Tris, pH 5.5, 1.5M ammonium sulphate, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54178 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: May 8, 2012
RadiationMonochromator: CU / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 1.3→42.05 Å / Num. all: 41039 / Num. obs: 38970 / % possible obs: 98.5 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2
Reflection shellResolution: 1.3→1.331 Å / % possible all: 96.17

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Processing

Software
NameVersionClassification
HKL-3000data collection
MLPHAREphasing
REFMAC5.6.0117refinement
HKL-3000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: SAD / Resolution: 1.3→42.05 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.952 / SU B: 0.794 / SU ML: 0.034 / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R: 0.057 / ESU R Free: 0.06 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.21969 2069 5 %RANDOM
Rwork0.19325 ---
obs0.1946 38970 96.17 %-
all-41039 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 16.42 Å2
Baniso -1Baniso -2Baniso -3
1--0.83 Å20 Å20 Å2
2--0.74 Å20 Å2
3---0.09 Å2
Refinement stepCycle: LAST / Resolution: 1.3→42.05 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1406 0 0 136 1542
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.0191505
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.2831.962057
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3175201
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.72824.34869
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.36915259
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.6231511
X-RAY DIFFRACTIONr_chiral_restr0.1460.2227
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.0211163
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.3→1.331 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.446 144 -
Rwork0.372 2300 -
obs--82.65 %

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