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- PDB-1tho: CRYSTAL STRUCTURE OF A MUTANT ESCHERICHIA COLI THIOREDOXIN WITH A... -

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Basic information

Entry
Database: PDB / ID: 1tho
TitleCRYSTAL STRUCTURE OF A MUTANT ESCHERICHIA COLI THIOREDOXIN WITH AN ARGININE INSERTION IN THE ACTIVE SITE
ComponentsTHIOREDOXIN
KeywordsELECTRON TRANSPORT
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 / Resolution: 2.3 Å
AuthorsNikkola, M. / Langsetmo, K. / Fuchs, J.A. / Eklund, H.
Citation
Journal: To be Published
Title: Crystal Structure of a Mutant Escherichia Coli Thioredoxin with an Arginine Insertion in the Active Site
Authors: Nikkola, M. / Langsetmo, K. / Fuchs, J.A. / Eklund, H.
#1: Journal: J.Mol.Biol. / Year: 1990
Title: The Refined Structure of E. Coli Thioredoxin
Authors: Katti, S.K. / Lemaster, D.M. / Eklund, H.
History
DepositionJan 28, 1993Processing site: BNL
Revision 1.0Oct 31, 1993Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 29, 2017Group: Derived calculations / Other
Category: pdbx_database_status / struct_conf / struct_conf_type
Item: _pdbx_database_status.process_site

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: THIOREDOXIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,9082
Polymers11,8451
Non-polymers641
Water46826
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)78.400, 78.400, 35.100
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61
Atom site foot note1: RESIDUE 76 IS A CIS PROLINE.

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Components

#1: Protein THIOREDOXIN /


Mass: 11844.580 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / References: UniProt: P0AA25
#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.: 26 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.63 Å3/Da / Density % sol: 53.19 %

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
RefinementRfactor Rwork: 0.173 / Rfactor obs: 0.173 / Highest resolution: 2.3 Å
Refinement stepCycle: LAST / Highest resolution: 2.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms833 0 1 26 860
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.016
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg3.28
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it

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