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- PDB-3f4s: Crystal structure of Wolbachia pipientis alpha-DsbA1 T172V -

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Basic information

Entry
Database: PDB / ID: 3f4s
TitleCrystal structure of Wolbachia pipientis alpha-DsbA1 T172V
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: 1.55 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 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Putative uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,7072
Polymers26,5571
Non-polymers1501
Water4,468248
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)70.730, 49.610, 69.0
Angle α, β, γ (deg.)90.000, 106.330, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-392-

HOH

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Components

#1: Protein Putative uncharacterized protein / alpha-DsbA1


Mass: 26556.721 Da / Num. of mol.: 1 / Mutation: T172V
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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 248 / 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: 2.19 Å3/Da / Density % sol: 43.77 %
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 7, 2006
RadiationMonochromator: OSMIC / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.55→66.33 Å / Num. obs: 31734 / % possible obs: 94.9 % / Redundancy: 2.9 % / Biso Wilson estimate: 23.36 Å2 / Rmerge(I) obs: 0.036 / Net I/σ(I): 15.1
Reflection shellResolution: 1.55→1.61 Å / Redundancy: 2 % / Rmerge(I) obs: 0.281 / Mean I/σ(I) obs: 2.6 / % possible all: 62

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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: 1.55→66.216 Å / Occupancy max: 1 / Occupancy min: 0 / FOM work R set: 0.888 / SU ML: 0.17 / Isotropic thermal model: isotropic and TLS / Cross valid method: THROUGHOUT / σ(F): 0.08 / Phase error: 18.29 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.194 3151 10.03 %random
Rwork0.151 28255 --
obs0.155 31406 93.95 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 69.991 Å2 / ksol: 0.363 e/Å3
Displacement parametersBiso max: 75.97 Å2 / Biso mean: 29.868 Å2 / Biso min: 12.59 Å2
Baniso -1Baniso -2Baniso -3
1-0.236 Å20 Å2-2.995 Å2
2---2.266 Å20 Å2
3----0.231 Å2
Refinement stepCycle: LAST / Resolution: 1.55→66.216 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1634 0 10 248 1892
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0051827
X-RAY DIFFRACTIONf_angle_d0.8862479
X-RAY DIFFRACTIONf_chiral_restr0.068267
X-RAY DIFFRACTIONf_plane_restr0.005321
X-RAY DIFFRACTIONf_dihedral_angle_d13.613696
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 23

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.55-1.5730.284860.2166475053
1.573-1.5980.224850.19383592062
1.598-1.6240.2021160.16928104474
1.624-1.6520.2661380.1571211134992
1.652-1.6820.2061530.1511234138797
1.682-1.7140.2171360.1311260139698
1.714-1.7490.2111250.1291290141598
1.749-1.7870.1911380.1211281141997
1.787-1.8290.1931170.1291294141198
1.829-1.8750.2011500.1231288143898
1.875-1.9250.1881600.1191237139798
1.925-1.9820.1931590.1181280143998
1.982-2.0460.1581420.1141284142699
2.046-2.1190.1671470.111283143099
2.119-2.2040.1791370.1161307144499
2.204-2.3040.1571490.11413071456100
2.304-2.4260.1781300.11613321462100
2.426-2.5780.1961610.12812941455100
2.578-2.7770.221420.13813101452100
2.777-3.0560.1741390.14613291468100
3.056-3.4980.1781350.13513261461100
3.498-4.4070.1521460.12913231469100
4.407-66.2770.1691600.15613581518100

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