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- PDB-4aj8: Crystallographic structure of thioredoxin from Litopenaeus vannam... -

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Basic information

Entry
Database: PDB / ID: 4aj8
TitleCrystallographic structure of thioredoxin from Litopenaeus vannamei (partially reduced).
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 / MOLECULAR REPLACEMENT / Resolution: 1.54 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 16, 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 1.4Oct 16, 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)24,67712
Polymers23,9172
Non-polymers76010
Water3,423190
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3030 Å2
ΔGint-23 kcal/mol
Surface area10560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.523, 57.523, 118.016
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-2026-

HOH

21A-2054-

HOH

31B-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 (NADPH)
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 5 / 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.: 190 / 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: 2.35 Å3/Da / Density % sol: 47.61 % / 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: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418
DetectorType: RIGAKU R-AXIS IV PLUS PLUS / Detector: IMAGE PLATE / Date: Aug 11, 2011 / Details: OSMIC BLUE
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.54→24.37 Å / Num. obs: 33397 / % possible obs: 99.7 % / Observed criterion σ(I): 0 / Redundancy: 6.3 % / Biso Wilson estimate: 18.2 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 6.6
Reflection shellResolution: 1.54→1.62 Å / Redundancy: 5.5 % / Rmerge(I) obs: 0.25 / Mean I/σ(I) obs: 3 / % possible all: 98.6

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Processing

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

3zzx


Resolution: 1.54→23.218 Å / SU ML: 0.21 / σ(F): 1.38 / Phase error: 20.29 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2152 1692 5.1 %
Rwork0.1783 --
obs0.1802 33366 99.84 %
Solvent computationShrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 48.172 Å2 / ksol: 0.393 e/Å3
Displacement parametersBiso mean: 21.21 Å2
Baniso -1Baniso -2Baniso -3
1-0.36 Å20 Å20 Å2
2--0.36 Å20 Å2
3----0.7199 Å2
Refinement stepCycle: LAST / Resolution: 1.54→23.218 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1664 0 49 190 1903
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0271971
X-RAY DIFFRACTIONf_angle_d2.3532664
X-RAY DIFFRACTIONf_dihedral_angle_d14.615772
X-RAY DIFFRACTIONf_chiral_restr0.156286
X-RAY DIFFRACTIONf_plane_restr0.012357
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5398-1.58510.29091210.22792579X-RAY DIFFRACTION98
1.5851-1.63620.25151440.21012611X-RAY DIFFRACTION100
1.6362-1.69470.23541400.21132611X-RAY DIFFRACTION100
1.6947-1.76250.2071230.19862610X-RAY DIFFRACTION100
1.7625-1.84270.26331430.19822658X-RAY DIFFRACTION100
1.8427-1.93980.24731500.19192615X-RAY DIFFRACTION100
1.9398-2.06130.22291650.18092623X-RAY DIFFRACTION100
2.0613-2.22030.20931270.17882651X-RAY DIFFRACTION100
2.2203-2.44350.20521530.17272621X-RAY DIFFRACTION100
2.4435-2.79660.23181420.18312668X-RAY DIFFRACTION100
2.7966-3.52150.19491480.17162668X-RAY DIFFRACTION100
3.5215-23.22040.20031360.16232759X-RAY DIFFRACTION100

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