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- PDB-5g2z: Crystallographic structure of mutant W31A of thioredoxin from Lit... -

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Basic information

Entry
Database: PDB / ID: 5g2z
TitleCrystallographic structure of mutant W31A of thioredoxin from Litopenaeus vannamei
ComponentsTHIOREDOXIN
KeywordsOXIDOREDUCTASE / THIOREDOXIN / SHRIMP / LITOPENAEUS VANNAMEI / MUTANT / 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
Biological speciesLITOPENAEUS VANNAMEI (Pacific white shrimp)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.88 Å
AuthorsCampos-Acevedo, A.A. / Rudino-Pinera, E.
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2017
Title: Is dimerization a common feature in thioredoxins? The case of thioredoxin from Litopenaeus vannamei.
Authors: Campos-Acevedo, A.A. / Sotelo-Mundo, R.R. / Perez, J. / Rudino-Pinera, E.
History
DepositionApr 18, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 15, 2017Provider: repository / Type: Initial release
Revision 1.1Apr 12, 2017Group: Database references
Revision 1.2Apr 19, 2017Group: Database references
Revision 1.3Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf
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

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Assembly

Deposited unit
A: THIOREDOXIN
B: THIOREDOXIN


Theoretical massNumber of molelcules
Total (without water)23,6872
Polymers23,6872
Non-polymers00
Water2,522140
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area710 Å2
ΔGint-8 kcal/mol
Surface area11050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)33.156, 62.675, 99.332
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein THIOREDOXIN


Mass: 11843.578 Da / Num. of mol.: 2 / Mutation: YES
Source method: isolated from a genetically manipulated source
Details: RESIDUE 11 IS A SER IN THE UNIPROT DEPOSIT B1PWB9, IN THIS STRUCTURE A PHE IS CLEARLY VISIBLE ON POSITION 11.
Source: (gene. exp.) LITOPENAEUS VANNAMEI (Pacific white shrimp)
Plasmid: PET22B / Production host: ESCHERICHIA COLI (E. coli)
References: UniProt: B1PWB9, thioredoxin-disulfide reductase (NADPH)
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 140 / 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 PHENILALANINE

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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: 2.15 Å3/Da / Density % sol: 42.78 % / Description: NONE
Crystal growpH: 7
Details: 30% (W/V) POLYETHYLENE GLYCOL 3, 000. 100 MM TRIS BASE/HYDROCHLORIC ACID PH 7.0. 200 MM NACL

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Wavelength: 1.5418
DetectorType: RIGAKU-MSC R-AXIS IV / Detector: IMAGE PLATE / Date: Nov 18, 2014 / 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→23.43 Å / Num. obs: 17415 / % possible obs: 99.4 % / Observed criterion σ(I): 0 / Redundancy: 4 % / Biso Wilson estimate: 23.21 Å2 / Rmerge(I) obs: 0.04 / Net I/σ(I): 17.6
Reflection shellResolution: 1.88→1.92 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.21 / Mean I/σ(I) obs: 4.6 / % possible all: 100

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Processing

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

3zzx


Resolution: 1.88→23.429 Å / SU ML: 0.2 / σ(F): 1.36 / Phase error: 22.19 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2364 1738 10 %
Rwork0.1842 --
obs0.1895 17375 99.17 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 28.26 Å2
Refinement stepCycle: LAST / Resolution: 1.88→23.429 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1648 0 0 140 1788
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071693
X-RAY DIFFRACTIONf_angle_d0.8382283
X-RAY DIFFRACTIONf_dihedral_angle_d15.9411067
X-RAY DIFFRACTIONf_chiral_restr0.055259
X-RAY DIFFRACTIONf_plane_restr0.005300
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.88-1.93530.26411420.20091281X-RAY DIFFRACTION100
1.9353-1.99780.27861420.19591281X-RAY DIFFRACTION100
1.9978-2.06910.28861470.20431317X-RAY DIFFRACTION100
2.0691-2.15190.2351390.1921254X-RAY DIFFRACTION100
2.1519-2.24980.2511430.18721283X-RAY DIFFRACTION99
2.2498-2.36830.22671460.18031314X-RAY DIFFRACTION99
2.3683-2.51650.2451420.1971274X-RAY DIFFRACTION99
2.5165-2.71060.27521450.20071309X-RAY DIFFRACTION99
2.7106-2.98280.28741450.19831307X-RAY DIFFRACTION100
2.9828-3.41330.21841460.19631316X-RAY DIFFRACTION99
3.4133-4.29610.2331460.15631314X-RAY DIFFRACTION98
4.2961-23.43060.19151550.17571387X-RAY DIFFRACTION97

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