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- PDB-4aj7: Crystallographic structure of thioredoxin from Litopenaeus vannam... -

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Basic information

Entry
Database: PDB / ID: 4aj7
TitleCrystallographic structure of thioredoxin from Litopenaeus vannamei (oxidized form).
ComponentsTHIOREDOXIN
KeywordsOXIDOREDUCTASE / DISULFIDE REDUCTION
Function / homology
Function and homology information


protein-disulfide reductase activity / metal ion binding
Similarity search - Function
Thioredoxin / Thioredoxin / 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
ACETATE ION / Thioredoxin
Similarity search - Component
Biological speciesLITOPENAEUS VANNAMEI (Pacific white shrimp)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.035 Å
AuthorsCampos-Acevedo, A.A. / Sotelo-Mundo, R.R. / Rudino-Pinera, E.
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2013
Title: Expression, Purification, Crystallization and X-Ray Crystallographic Studies of Different Redox States of the Active Site of Thioredoxin 1 from the Whiteleg Shrimp Litopenaeus Vannamei
Authors: Campos-Acevedo, A.A. / Garcia-Orozco, K.D. / Sotelo-Mundo, R.R. / Rudino-Pinera, E.
History
DepositionFeb 15, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 6, 2013Provider: repository / Type: Initial release
Revision 1.1May 15, 2013Group: Database references
Revision 1.2Jun 5, 2013Group: Database references
Revision 1.3Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: THIOREDOXIN
B: THIOREDOXIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,3758
Polymers23,9172
Non-polymers4576
Water1,982110
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2280 Å2
ΔGint-18.3 kcal/mol
Surface area10550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.895, 57.895, 117.869
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number153
Space group name H-MP3212
Components on special symmetry positions
IDModelComponents
11A-2017-

HOH

21B-2029-

HOH

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Components

#1: Protein THIOREDOXIN


Mass: 11958.710 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) LITOPENAEUS VANNAMEI (Pacific white shrimp)
Production host: ESCHERICHIA COLI (E. coli)
References: UniProt: B1PWB9, thioredoxin-disulfide reductase
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 110 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsA SERINE IS PRESENT IN RESIDUE 11 FROM UNIPROT DEPOSIT B1PWB9, IN OUR STRUCTURE RESIDUE 11 IS A PHENYLALANINE.

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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: 2.37 Å3/Da / Density % sol: 48.19 % / Description: NONE
Crystal growpH: 4.6
Details: 2.0 M AMMONIUM SUPHATE, 0.1 M SODIUM ACETATE, PH 4.6

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X6A / Wavelength: 0.98
DetectorType: ADSC CCD / Detector: CCD / Date: Dec 8, 2011
Details: DOUBLE CRYSTAL CHANNEL CUT, SI(111), 1M LONG RH COATED TOROIDAL MIRROR FOR VERTICAL AND HORIZONTAL FOCUSING.
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.04→19.64 Å / Num. obs: 14756 / % possible obs: 99.4 % / Observed criterion σ(I): 0 / Redundancy: 6.4 % / Biso Wilson estimate: 24.42 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 3.1
Reflection shellResolution: 2.04→2.15 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.24 / Mean I/σ(I) obs: 3.1 / % possible all: 96.6

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3ZZX

3zzx


Resolution: 2.035→19.094 Å / SU ML: 0.27 / σ(F): 1.4 / Phase error: 19.93 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2249 747 5.1 %
Rwork0.1742 --
obs0.1768 14719 99.47 %
Solvent computationShrinkage radii: 0.98 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 41.744 Å2 / ksol: 0.404 e/Å3
Displacement parametersBiso mean: 24.73 Å2
Baniso -1Baniso -2Baniso -3
1-0.25 Å20 Å20 Å2
2--0.25 Å20 Å2
3----0.5 Å2
Refinement stepCycle: LAST / Resolution: 2.035→19.094 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1664 0 29 110 1803
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0091873
X-RAY DIFFRACTIONf_angle_d1.0662527
X-RAY DIFFRACTIONf_dihedral_angle_d14.254733
X-RAY DIFFRACTIONf_chiral_restr0.067276
X-RAY DIFFRACTIONf_plane_restr0.005333
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0352-2.19220.24831620.19682678X-RAY DIFFRACTION97
2.1922-2.41240.22681390.17312806X-RAY DIFFRACTION100
2.4124-2.76060.26431660.17442785X-RAY DIFFRACTION100
2.7606-3.47460.191350.16782801X-RAY DIFFRACTION100
3.4746-19.0950.22051450.17332902X-RAY DIFFRACTION100

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