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- PDB-3zzx: Crystallographic structure of thioredoxin from Litopenaeus vannamei -

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Basic information

Entry
Database: PDB / ID: 3zzx
TitleCrystallographic structure of thioredoxin from Litopenaeus vannamei
ComponentsTHIOREDOXIN
KeywordsOXIDOREDUCTASE
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 / (2R,3S)-1,4-DIMERCAPTOBUTANE-2,3-DIOL / Thioredoxin
Similarity search - Component
Biological speciesLITOPENAEUS VANNAMEI (Pacific white shrimp)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.88 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
DepositionSep 5, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 26, 2012Provider: 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 6, 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: THIOREDOXIN
B: THIOREDOXIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,94915
Polymers23,9172
Non-polymers1,03213
Water1,892105
1
A: THIOREDOXIN
B: THIOREDOXIN
hetero molecules

A: THIOREDOXIN
B: THIOREDOXIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,89930
Polymers47,8354
Non-polymers2,06426
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555-x+y,y,-z+2/31
Buried area8340 Å2
ΔGint-60.6 kcal/mol
Surface area20100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.776, 57.776, 118.094
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-2021-

HOH

21B-2028-

HOH

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Components

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Protein , 1 types, 2 molecules AB

#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) / Strain (production host): BL21
References: UniProt: B1PWB9, thioredoxin-disulfide reductase

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Non-polymers , 5 types, 118 molecules

#2: Chemical ChemComp-DTU / (2R,3S)-1,4-DIMERCAPTOBUTANE-2,3-DIOL


Mass: 154.251 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O2S2
#3: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-SO4 / SULFATE ION


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


Mass: 18.015 Da / Num. of mol.: 105 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.49 Å3/Da / Density % sol: 50.6 % / Description: DATA WERE COLLECTED AT LANEM
Crystal growpH: 4.6
Details: 2.0 M AMMONIUM SULPHATE, 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-MSC R-AXIS IV++ / Detector: IMAGE PLATE / Date: Aug 11, 2011 / Details: VARIMAX-HR
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.88→25 Å / Num. obs: 55281 / % possible obs: 94.5 % / Observed criterion σ(I): 0 / Redundancy: 3.14 % / Biso Wilson estimate: 23.81 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 13.3
Reflection shellResolution: 1.88→1.99 Å / Redundancy: 3.16 % / Rmerge(I) obs: 0.44 / Mean I/σ(I) obs: 3.14 / % possible all: 91.6

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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 1XWA

1xwa


Resolution: 1.88→23.29 Å / SU ML: 0.51 / σ(F): 1.36 / Phase error: 23.24 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2312 907 5.1 %
Rwork0.1822 --
obs0.1847 17729 95.01 %
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 50.292 Å2 / ksol: 0.384 e/Å3
Displacement parametersBiso mean: 25.8 Å2
Baniso -1Baniso -2Baniso -3
1-0.2403 Å20 Å20 Å2
2--0.2403 Å20 Å2
3----0.4806 Å2
Refinement stepCycle: LAST / Resolution: 1.88→23.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1664 0 65 105 1834
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071894
X-RAY DIFFRACTIONf_angle_d1.0262554
X-RAY DIFFRACTIONf_dihedral_angle_d15.425739
X-RAY DIFFRACTIONf_chiral_restr0.072279
X-RAY DIFFRACTIONf_plane_restr0.004338
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8802-1.99790.30631550.27152679X-RAY DIFFRACTION92
1.9979-2.15210.29491530.21232717X-RAY DIFFRACTION93
2.1521-2.36850.26111340.18912754X-RAY DIFFRACTION94
2.3685-2.71080.22811630.18122803X-RAY DIFFRACTION95
2.7108-3.41360.24941560.1792860X-RAY DIFFRACTION97
3.4136-23.29140.18451460.16243009X-RAY DIFFRACTION98

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