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- PDB-1txx: ACTIVE-SITE VARIANT OF E.COLI THIOREDOXIN -

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Basic information

Entry
Database: PDB / ID: 1txx
TitleACTIVE-SITE VARIANT OF E.COLI THIOREDOXIN
ComponentsPROTEIN (THIOREDOXIN)
KeywordsOXIDOREDUCTASE / REDOX / CXXC
Function / homology
Function and homology information


DNA polymerase processivity factor activity / protein-disulfide reductase activity / cell redox homeostasis / cytosol / cytoplasm
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 1
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsSchultz, L.W. / Chivers, P.T. / Raines, R.T.
Citation
Journal: Acta Crystallogr.,Sect.D / Year: 1999
Title: The CXXC motif: crystal structure of an active-site variant of Escherichia coli thioredoxin.
Authors: Schultz, L.W. / Chivers, P.T. / Raines, R.T.
#1: Journal: Embo J. / Year: 1996
Title: The Cxxc Motif: Imperatives for the Formation of Native Disulfide Bonds
Authors: Chivers, P.T. / Labiossiere, M.C.A. / Raines, R.T.
History
DepositionApr 7, 1999Deposition site: BNL / Processing site: RCSB
Revision 1.0Sep 13, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 4, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software / Item: _software.classification / _software.name
Revision 1.4Mar 14, 2018Group: Database references / Category: struct_ref_seq_dif / Item: _struct_ref_seq_dif.details
Revision 1.5Aug 23, 2023Group: Advisory / Data collection ...Advisory / 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_unobs_or_zero_occ_atoms / 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 / _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_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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PROTEIN (THIOREDOXIN)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,8822
Polymers11,8191
Non-polymers641
Water1,45981
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)42.530, 42.530, 105.240
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein PROTEIN (THIOREDOXIN)


Mass: 11818.562 Da / Num. of mol.: 1 / Mutation: P33V, G34W
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Cellular location: CYTOPLASM / Species (production host): Escherichia coli / Cellular location (production host): PERIPLASM / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21DE3 / Keywords: OXIDOREDUCTASE
References: UniProt: P0AA25, Oxidoreductases; Acting on a sulfur group of donors
#2: Chemical ChemComp-CU / COPPER (II) ION / Copper


Mass: 63.546 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cu
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 81 / Source method: isolated from a natural source / Formula: H2O

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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: 2.01 Å3/Da / Density % sol: 37 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 4.2
Details: DROPS (6 ML) OF 0.050 M SODIUM SUCCINATE BUFFER, PH 4.2, CONTAINING CVWC THIOREDOXIN (10 MG/ML), METHYL-ETHER PEG2000 (10% W/V) AND CUPRIC ACETATE (1 MM) WERE SUSPENDED OVER 1.0 ML WELLS OF ...Details: DROPS (6 ML) OF 0.050 M SODIUM SUCCINATE BUFFER, PH 4.2, CONTAINING CVWC THIOREDOXIN (10 MG/ML), METHYL-ETHER PEG2000 (10% W/V) AND CUPRIC ACETATE (1 MM) WERE SUSPENDED OVER 1.0 ML WELLS OF 0.10 M SODIUM SUCCINATE BUFFER, PH 4.2, CONTAINING METHYL-ETHER PEG 2000 (20% W/V) AND CUPRIC ACETATE (2 MM)., VAPOR DIFFUSION, HANGING DROP
Crystal
*PLUS
Crystal grow
*PLUS
Temperature: 293 K
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
10.050 Msodium succinate1drop
210 mg/mlprotein1drop
310 %(w/v)mPEG20001drop
41 mMcopper(II) acetate1drop
50.10 Msodium succinate1reservoir
620 %(w/v)mPEG20001reservoir
72 mg/mlcopper(II) acetate1reservoir

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Data collection

DiffractionMean temperature: 277 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: SIEMENS / Detector: AREA DETECTOR / Date: Dec 11, 1996 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.2→30 Å / Num. obs: 5979 / % possible obs: 98 % / Observed criterion σ(I): 0.33 / Redundancy: 6.3 % / Rsym value: 0.083 / Net I/σ(I): 20
Reflection shellResolution: 2.2→2.3 Å / Redundancy: 3 % / Rsym value: 0.173 / % possible all: 95
Reflection
*PLUS
% possible obs: 98 % / Num. measured all: 37820 / Rmerge(I) obs: 0.083
Reflection shell
*PLUS
% possible obs: 95 % / Rmerge(I) obs: 0.173

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Processing

Software
NameVersionClassification
XDSdata scaling
XSCALIBREdata reduction
AMoREphasing
TNT5Drefinement
XDSdata reduction
XSCALIBREdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2TRX

2trx


Resolution: 2.2→30 Å / σ(F): 0 / Stereochemistry target values: TNT PROTGEO
RfactorNum. reflection% reflection
Rwork0.171 --
obs-37820 98 %
Solvent computationBsol: 275 Å2 / ksol: 0.82 e/Å3
Refinement stepCycle: LAST / Resolution: 2.2→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms832 0 1 81 914
Refine LS restraints
Refine-IDTypeDev idealNumberWeight
X-RAY DIFFRACTIONt_bond_d0.0118508
X-RAY DIFFRACTIONt_angle_deg2.27115112
X-RAY DIFFRACTIONt_dihedral_angle_d19.2435060
X-RAY DIFFRACTIONt_incorr_chiral_ct0
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes0.0052425
X-RAY DIFFRACTIONt_gen_planes0.0111850
X-RAY DIFFRACTIONt_it
X-RAY DIFFRACTIONt_nbd0.0361950
Software
*PLUS
Name: TNT / Version: 5D / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.2 Å / σ(F): 0 / Rfactor obs: 0.171
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeWeightDev ideal
X-RAY DIFFRACTIONt_bond_d8
X-RAY DIFFRACTIONt_angle_deg12
X-RAY DIFFRACTIONt_dihedral_angle_d0
X-RAY DIFFRACTIONt_planar_d250.005
X-RAY DIFFRACTIONt_plane_restr500.01

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