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- PDB-4v2l: Crystallographic structure of thioredoxin from Litopenaeus vannam... -

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Basic information

Entry
Database: PDB / ID: 4v2l
TitleCrystallographic structure of thioredoxin from Litopenaeus vannamei: Radiation damage effect at 3.4 MGy, focused in disulfide bonds.
ComponentsTHIOREDOXIN
KeywordsOXIDOREDUCTASE / THIOREDOXIN / SHRIMP / LITOPENAEUS VANNAMIE / RADIATION DAMAGE / DISULFIDE BOND
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: 1.65 Å
AuthorsCampos-Acevedo, A.A. / Rudino-Pinera, E.
CitationJournal: Molecules / Year: 2014
Title: Crystallographic Studies Evidencing the High Energy Tolerance to Disrupting the Interface Disulfide Bond of Thioredoxin 1 from White Leg Shrimp Litopenaeus Vannamei.
Authors: Campos-Acevedo, A.A. / Rudino-Pinera, E.
History
DepositionOct 10, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 14, 2015Provider: repository / Type: Initial release
Revision 1.1Jan 10, 2024Group: 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 1.2Oct 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)24,2576
Polymers23,9172
Non-polymers3394
Water3,495194
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2060 Å2
ΔGint-19.6 kcal/mol
Surface area10400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.182, 57.182, 117.619
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-2037-

HOH

21B-2034-

HOH

31B-2049-

HOH

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Components

#1: Protein THIOREDOXIN


Mass: 11958.710 Da / Num. of mol.: 2 / Mutation: YES
Source method: isolated from a genetically manipulated source
Details: RESIDUE 11 IS SER IN UNIPROT DEPOSIT B1PWB9, IN THIS STRUCTURE A PHE IS CLEARLY VISIBLE ON POSITION 11.
Source: (gene. exp.) LITOPENAEUS VANNAMEI (Pacific white shrimp)
Plasmid: PET11A / 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.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 194 / 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: 2.31 Å3/Da / Density % sol: 46.81 % / Description: NONE
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: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9686
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 23, 2012 / Details: MIRRORS
RadiationMonochromator: SI 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9686 Å / Relative weight: 1
ReflectionResolution: 1.65→28.59 Å / Num. obs: 26586 / % possible obs: 99.9 % / Observed criterion σ(I): 0 / Redundancy: 3.3 % / Biso Wilson estimate: 24.97 Å2 / Rmerge(I) obs: 0.04 / Net I/σ(I): 15.9
Reflection shellResolution: 1.65→1.72 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.43 / Mean I/σ(I) obs: 2.4 / % possible all: 99.8

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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: 1.65→27.782 Å / SU ML: 0.2 / σ(F): 1.37 / Phase error: 22.4 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2239 1342 5.1 %
Rwork0.1853 --
obs0.1872 26572 98.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 31.6 Å2
Refinement stepCycle: LAST / Resolution: 1.65→27.782 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1664 0 21 194 1879
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071856
X-RAY DIFFRACTIONf_angle_d0.9912503
X-RAY DIFFRACTIONf_dihedral_angle_d13.892727
X-RAY DIFFRACTIONf_chiral_restr0.04275
X-RAY DIFFRACTIONf_plane_restr0.004327
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6501-1.7090.28231450.26442518X-RAY DIFFRACTION100
1.709-1.77740.25561310.24832508X-RAY DIFFRACTION100
1.7774-1.85830.3191350.23282496X-RAY DIFFRACTION100
1.8583-1.95630.25271270.20652546X-RAY DIFFRACTION100
1.9563-2.07880.2481260.19342524X-RAY DIFFRACTION100
2.0788-2.23920.22181250.19312535X-RAY DIFFRACTION100
2.2392-2.46440.20431490.18722502X-RAY DIFFRACTION99
2.4644-2.82080.22671550.19522527X-RAY DIFFRACTION99
2.8208-3.55270.21761370.17792539X-RAY DIFFRACTION98
3.5527-27.78590.2041120.16172535X-RAY DIFFRACTION95

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