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- PDB-1nw2: The crystal structure of the mutant R82E of Thioredoxin from Alic... -

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Basic information

Entry
Database: PDB / ID: 1nw2
TitleThe crystal structure of the mutant R82E of 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
ACETATE ION / CACODYLATE ION / Thioredoxin
Similarity search - Component
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
DepositionFeb 5, 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: Non-polymer description / Version format compliance
Revision 1.3Oct 27, 2021Group: Data collection / Database references / Derived calculations
Category: database_2 / diffrn_source ...database_2 / diffrn_source / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
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
E: THIOREDOXIN
F: THIOREDOXIN
G: THIOREDOXIN
H: THIOREDOXIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,85228
Polymers92,4588
Non-polymers1,39420
Water12,016667
1
A: THIOREDOXIN
B: THIOREDOXIN
C: THIOREDOXIN
D: THIOREDOXIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,12516
Polymers46,2294
Non-polymers89612
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6410 Å2
ΔGint-192 kcal/mol
Surface area17960 Å2
MethodPISA
2
E: THIOREDOXIN
F: THIOREDOXIN
G: THIOREDOXIN
H: THIOREDOXIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,72712
Polymers46,2294
Non-polymers4988
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6270 Å2
ΔGint-164 kcal/mol
Surface area18080 Å2
MethodPISA
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15160 Å2
ΔGint-390 kcal/mol
Surface area33560 Å2
MethodPISA
4
A: THIOREDOXIN
B: THIOREDOXIN
C: THIOREDOXIN
D: THIOREDOXIN
hetero molecules

E: THIOREDOXIN
F: THIOREDOXIN
G: THIOREDOXIN
H: THIOREDOXIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,85228
Polymers92,4588
Non-polymers1,39420
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_545x,y-1,z1
Buried area13480 Å2
ΔGint-365 kcal/mol
Surface area35240 Å2
MethodPISA
5
A: THIOREDOXIN
B: THIOREDOXIN
C: THIOREDOXIN
D: THIOREDOXIN
hetero molecules

E: THIOREDOXIN
F: THIOREDOXIN
G: THIOREDOXIN
H: THIOREDOXIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,85228
Polymers92,4588
Non-polymers1,39420
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_746-x+2,y-1/2,-z+11
Buried area13460 Å2
ΔGint-372 kcal/mol
Surface area35260 Å2
MethodPISA
6
A: THIOREDOXIN
B: THIOREDOXIN
C: THIOREDOXIN
D: THIOREDOXIN
hetero molecules

E: THIOREDOXIN
F: THIOREDOXIN
G: THIOREDOXIN
H: THIOREDOXIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,85228
Polymers92,4588
Non-polymers1,39420
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_455x-1,y,z1
Buried area13160 Å2
ΔGint-356 kcal/mol
Surface area35560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.61, 60.21, 82.95
Angle α, β, γ (deg.)90.00, 93.30, 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: 11557.211 Da / Num. of mol.: 8 / Mutation: R82E
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 (NADPH)
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical ChemComp-CAC / CACODYLATE ION / dimethylarsinate


Mass: 136.989 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6AsO2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 667 / 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: 1.97 Å3/Da / Density % sol: 37 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8
Details: Peg 8000, calcium acetate, CACODYLATE, VAPOR DIFFUSION, HANGING DROP, temperature 295K
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
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: 52158 / Num. obs: 52158 / % possible obs: 84.1 % / Observed criterion σ(I): 0 / Rsym value: 0.051 / Net I/σ(I): 20.1
Reflection shellResolution: 1.9→1.97 Å / Mean I/σ(I) obs: 4.3 / Rsym value: 0.262 / % possible all: 85.7
Reflection
*PLUS
Num. measured all: 234705 / Rmerge(I) obs: 0.051
Reflection shell
*PLUS
% possible obs: 85.7 % / Rmerge(I) obs: 0.262

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNS1.1refinement
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
Rfree0.255 5263 10 %RANDOM
Rwork0.212 ---
all0.228 52158 --
obs0.228 52158 --
Refinement stepCycle: LAST / Resolution: 1.9→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6480 0 55 667 7202
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_angle_deg1.56
Refinement
*PLUS
% reflection Rfree: 5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS

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