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- PDB-1nsw: The Crystal Structure of the K18G Mutant of the thioredoxin from ... -

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Basic information

Entry
Database: PDB / ID: 1nsw
TitleThe Crystal Structure of the K18G Mutant of the thioredoxin from Alicyclobacillus acidocaldarius
ComponentsTHIOREDOXIN
KeywordsELECTRON TRANSPORT / Thermostability / thioredoxin
Function / homology
Function and homology information


protein-disulfide reductase activity / cell redox homeostasis / cytosol
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 speciesAlicyclobacillus acidocaldarius (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsBartolucci, S. / De Simone, G. / Galdiero, S. / Improta, R. / Menchise, V. / Pedone, C. / Pedone, E. / Saviano, M.
Citation
Journal: J.Bacteriol. / Year: 2003
Title: An integrated structural and computational study of the thermostability of two thioredoxin mutants from Alicyclobacillus acidocaldarius
Authors: Bartolucci, S. / De Simone, G. / Galdiero, S. / Improta, R. / Menchise, V. / Pedone, C. / Pedone, E. / Saviano, M.
#1: Journal: Biochem.J. / Year: 1999
Title: Prediction and Experimental Testing of Bacillus acidocaldarius Thioredoxin Stability.
Authors: Pedone, E. / Cannio, R. / Saviano, M. / Rossi, M. / Bartolucci, S.
History
DepositionJan 28, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 5, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 27, 2021Group: Data collection / Database references / Category: database_2 / diffrn_source / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _struct_ref_seq_dif.details
Revision 1.4Aug 16, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.5Oct 30, 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
C: THIOREDOXIN
D: THIOREDOXIN


Theoretical massNumber of molelcules
Total (without water)46,0534
Polymers46,0534
Non-polymers00
Water4,360242
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4010 Å2
ΔGint-28 kcal/mol
Surface area19350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.73, 73.89, 54.91
Angle α, β, γ (deg.)90.00, 103.79, 90.00
Int Tables number4
Cell settingmonoclinic
Space group name H-MP1211

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Components

#1: Protein
THIOREDOXIN / E.C.1.8.1.9 / TRX


Mass: 11513.163 Da / Num. of mol.: 4 / Mutation: K18G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Alicyclobacillus acidocaldarius (bacteria)
Production host: Escherichia coli (E. coli)
References: UniProt: P80579, thioredoxin-disulfide reductase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 242 / Source method: isolated from a natural source / Formula: H2O
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: 1.9 Å3/Da / Density % sol: 34.7 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8
Details: Hepes, PEG 8000, Calcium acetate, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal grow
*PLUS
Temperature: 22 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
116 mg/mlprotein1drop
20.1 MHEPES1reservoirpH8.
325 %PEG80001reservoir
40.2 Mcalcium acetate1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.9072 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Sep 20, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9072 Å / Relative weight: 1
ReflectionResolution: 1.9→20 Å / Num. all: 26867 / Num. obs: 26867 / % possible obs: 93.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rsym value: 0.03 / Net I/σ(I): 25.5
Reflection shellResolution: 1.9→1.97 Å / Mean I/σ(I) obs: 7.09 / Rsym value: 0.115 / % possible all: 95.6
Reflection
*PLUS
Num. obs: 26803 / Num. measured all: 120205 / Rmerge(I) obs: 0.03
Reflection shell
*PLUS
% possible obs: 95.6 % / Rmerge(I) obs: 0.115

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNS1refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2TRX

2trx


Resolution: 1.9→20 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.249 1350 -RANDOM
Rwork0.205 ---
obs0.237 26803 93.7 %-
all-26803 --
Refinement stepCycle: LAST / Resolution: 1.9→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3228 0 0 242 3470
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_angle_deg1.64
Refinement
*PLUS
% reflection Rfree: 5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS

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