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- PDB-5hr0: Crystal structure of thioredoxin E101G mutant -

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Basic information

Entry
Database: PDB / ID: 5hr0
TitleCrystal structure of thioredoxin E101G mutant
ComponentsThioredoxin
KeywordsOXIDOREDUCTASE / E. coli thioredoxin / thiol-redox reactions
Function / homology
Function and homology information


DNA polymerase processivity factor activity / protein-disulfide reductase activity / cell redox homeostasis / cytoplasm / 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
COPPER (II) ION / Thioredoxin / Thioredoxin 1
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.31 Å
AuthorsNoguera, M.E. / Vazquez, D.S. / Howard, E.I. / Cousido-Siah, A. / Mitschler, A. / Podjarny, A. / Santos, J.
CitationJournal: Sci Rep / Year: 2017
Title: Structural variability of E. coli thioredoxin captured in the crystal structures of single-point mutants.
Authors: Noguera, M.E. / Vazquez, D.S. / Ferrer-Sueta, G. / Agudelo, W.A. / Howard, E. / Rasia, R.M. / Manta, B. / Cousido-Siah, A. / Mitschler, A. / Podjarny, A. / Santos, J.
History
DepositionJan 22, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 22, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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.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.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr1_label_alt_id / _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_symmetry
Revision 1.2Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Thioredoxin
B: Thioredoxin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,7476
Polymers23,4932
Non-polymers2544
Water3,063170
1
A: Thioredoxin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,8743
Polymers11,7471
Non-polymers1272
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Thioredoxin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,8743
Polymers11,7471
Non-polymers1272
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)50.043, 50.043, 163.291
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11A-355-

HOH

21A-402-

HOH

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Components

#1: Protein Thioredoxin


Mass: 11746.521 Da / Num. of mol.: 2 / Mutation: E101G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: trxA, BN17_37301, ECs4714 / Production host: Escherichia coli (E. coli) / References: UniProt: C3SKR2, UniProt: P0AA25*PLUS
#2: Chemical
ChemComp-CU / COPPER (II) ION


Mass: 63.546 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cu
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 170 / 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: 2.51 Å3/Da / Density % sol: 51.04 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop
Details: The drop was a 1:1 mix of protein (18 mg/ml in water) and reservoir solution (100 mM sodium acetate, 4 mM CuSO4, 15 % ethanol, pH 4.75)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 0.9191 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Jul 8, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9191 Å / Relative weight: 1
ReflectionResolution: 1.31→19.862 Å / Num. obs: 57845 / % possible obs: 99.6 % / Redundancy: 5.4 % / Biso Wilson estimate: 15.64 Å2 / Rmerge(I) obs: 0.055 / Χ2: 1.043 / Net I/σ(I): 17 / Num. measured all: 588774
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
1.31-1.3650.451109951.01999.9
1.36-1.415.30.354109351.043100
1.41-1.485.40.244110091.055100
1.48-1.555.40.163109911.048100
1.55-1.655.40.119109501.058100
1.65-1.785.40.092109911.068100
1.78-1.965.40.067109771.047100
1.96-2.245.50.064109871.053100
2.24-2.825.60.067110041.023100
2.82-505.50.038106041.01596.1

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIXdev_2247refinement
PDB_EXTRACT3.15data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2TRX

2trx


Resolution: 1.31→19.862 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / Phase error: 18.96 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2092 2926 5.06 %random
Rwork0.1739 54919 --
obs0.1757 57845 99.51 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 66.62 Å2 / Biso mean: 22.3423 Å2 / Biso min: 9.05 Å2
Refinement stepCycle: final / Resolution: 1.31→19.862 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1628 0 4 170 1802
Biso mean--32.73 30.42 -
Num. residues----215
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0112003
X-RAY DIFFRACTIONf_angle_d1.0952723
X-RAY DIFFRACTIONf_chiral_restr0.085320
X-RAY DIFFRACTIONf_plane_restr0.008349
X-RAY DIFFRACTIONf_dihedral_angle_d16.371735
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 21

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.3103-1.33170.28911250.21442508263398
1.3317-1.35470.26361260.203326532779100
1.3547-1.37930.23471260.191925582684100
1.3793-1.40580.27161470.184825502697100
1.4058-1.43450.24891350.176826392774100
1.4345-1.46570.21691340.175625882722100
1.4657-1.49980.23141430.172425672710100
1.4998-1.53730.20581580.162925762734100
1.5373-1.57880.18851230.156826282751100
1.5788-1.62530.2331460.161725942740100
1.6253-1.67770.21531340.164426292763100
1.6777-1.73760.19451400.163426232763100
1.7376-1.80720.20091470.160625912738100
1.8072-1.88940.19131480.156125992747100
1.8894-1.98890.21771420.160326352777100
1.9889-2.11340.22441320.16526272759100
2.1134-2.27630.18321480.160826552803100
2.2763-2.5050.19691460.165326572803100
2.505-2.86650.20741350.184126772812100
2.8665-3.6080.21741430.187727222865100
3.608-19.86430.20211480.18062643279193

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