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- PDB-3f4t: Crystal structure of Wolbachia pipientis alpha-DsbA1 C97A/C146A -

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Basic information

Entry
Database: PDB / ID: 3f4t
TitleCrystal structure of Wolbachia pipientis alpha-DsbA1 C97A/C146A
ComponentsPutative uncharacterized protein
KeywordsOXIDOREDUCTASE / thioredoxin-fold / DSBA
Function / homology
Function and homology information


protein-disulfide reductase (glutathione) activity / protein disulfide isomerase activity / periplasmic space
Similarity search - Function
Ribonucleotide Reductase Protein R1; domain 1 - #80 / Thioredoxin / Ribonucleotide Reductase Protein R1; domain 1 / Thioredoxin-like fold / Glutaredoxin / Glutaredoxin / Thioredoxin-like superfamily / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
TRIETHYLENE GLYCOL / Thioredoxin-like fold domain-containing protein
Similarity search - Component
Biological speciesWolbachia pipientis (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsKurz, M. / Heras, B. / Martin, J.L.
CitationJournal: ANTIOXID.REDOX SIGNAL. / Year: 2009
Title: Structural and Functional Characterization of the Oxidoreductase alpha-DsbA1 from Wolbachia pipientis.
Authors: Kurz, M. / Iturbe-Ormaetxe, I. / Jarrott, R. / Shouldice, S.R. / Wouters, M.A. / Frei, P. / Glockshuber, R. / O'Neill, S.L. / Heras, B. / Martin, J.L.
History
DepositionNov 2, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 24, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.2Nov 10, 2021Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Nov 1, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.4Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature
Revision 1.5Apr 30, 2025Group: Database references / Category: citation / Item: _citation.title

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Putative uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,8833
Polymers26,4951
Non-polymers3882
Water3,261181
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)71.0, 49.5, 69.3
Angle α, β, γ (deg.)90.000, 106, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-1347-

HOH

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Components

#1: Protein Putative uncharacterized protein / alpha-DsbA1


Mass: 26494.564 Da / Num. of mol.: 1 / Mutation: C97A, C146A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Wolbachia pipientis (bacteria) / Strain: wMel / Gene: WD_1055 / Plasmid: pET42a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: Q73GA4
#2: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#3: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 181 / 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: 1

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Sample preparation

CrystalDensity Matthews: 2.21 Å3/Da / Density % sol: 44.32 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 22% PEG 3350, 0.1M Ammonium citrate pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
PH range: 5.5-5.9

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Sep 14, 2006
RadiationMonochromator: OSMIC / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.85→40.1 Å / Num. obs: 19850 / % possible obs: 99.9 % / Redundancy: 4.1 % / Biso Wilson estimate: 26.79 Å2 / Rmerge(I) obs: 0.056 / Net I/σ(I): 11.7
Reflection shellResolution: 1.85→1.92 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.38 / Mean I/σ(I) obs: 2.6 / % possible all: 99.7

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Processing

Software
NameVersionClassificationNB
PHENIXrefinement
PDB_EXTRACT3.006data extraction
CrystalCleardata collection
CrystalCleardata reduction
CrystalCleardata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3F4R

3f4r


Resolution: 1.85→40.059 Å / Occupancy max: 1 / Occupancy min: 0 / FOM work R set: 0.867 / SU ML: 0.24 / Isotropic thermal model: isotropic and TLS / Cross valid method: THROUGHOUT / σ(F): 0.07 / Phase error: 20.36 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.21 945 4.83 %random
Rwork0.172 18601 --
obs0.174 19546 98.33 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 72.374 Å2 / ksol: 0.377 e/Å3
Displacement parametersBiso max: 99.68 Å2 / Biso mean: 30.878 Å2 / Biso min: 10.02 Å2
Baniso -1Baniso -2Baniso -3
1-0.612 Å20 Å2-2.351 Å2
2--0.32 Å20 Å2
3----0.932 Å2
Refinement stepCycle: LAST / Resolution: 1.85→40.059 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1640 0 26 181 1847
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061761
X-RAY DIFFRACTIONf_angle_d0.9192373
X-RAY DIFFRACTIONf_chiral_restr0.07257
X-RAY DIFFRACTIONf_plane_restr0.005299
X-RAY DIFFRACTIONf_dihedral_angle_d14.587664
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 7

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.85-1.9480.2571170.2152566268395
1.948-2.070.2711220.1962656277898
2.07-2.2290.2411380.1842623276199
2.229-2.4540.1881510.1672645279699
2.454-2.8090.2251230.1722680280399
2.809-3.5380.2141400.1592674281499
3.538-40.0680.1721540.15227572911100
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)
11.08990.1334-0.29830.79340.02890.4393-0.0161-0.2302-0.0080.1358-0.0419-0.16010.00890.02780.04780.13590.0061-0.02330.14920.00460.11911.06643.193914.1717
20.4011-0.0050.01620.44010.00350.2528-0.0037-0.11190.12760.06140.0069-0.0835-0.11070.0342-0.00730.16190.0095-0.01290.1754-0.0210.17810.53354.604210.3401
31.99795.70682.00325.20254.84119.42050.2361-0.89831.2492-1.7561-0.59960.44550.6869-0.24290.35720.42430.0857-0.03050.26920.00190.389-1.9536-0.02880.6287
45.6016-3.91172.18751.5013-0.90291.04830.12660.05760.17950.16840.2091-0.0076-0.0139-0.0258-0.28030.71320.0430.1520.24130.04330.526117.962117.64028.3714
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A and resid 19:218
2X-RAY DIFFRACTION2chain A and resid 1001:1348
3X-RAY DIFFRACTION3chain A and resid 227
4X-RAY DIFFRACTION4chain A and resid 228

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