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- PDB-2trx: CRYSTAL STRUCTURE OF THIOREDOXIN FROM ESCHERICHIA COLI AT 1.68 AN... -

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Basic information

Entry
Database: PDB / ID: 2trx
TitleCRYSTAL STRUCTURE OF THIOREDOXIN FROM ESCHERICHIA COLI AT 1.68 ANGSTROMS RESOLUTION
ComponentsTHIOREDOXIN
KeywordsELECTRON TRANSPORT
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 1
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / Resolution: 1.68 Å
AuthorsKatti, S.K. / Lemaster, D.M. / Eklund, H.
Citation
Journal: J.Mol.Biol. / Year: 1990
Title: Crystal structure of thioredoxin from Escherichia coli at 1.68 A resolution.
Authors: Katti, S.K. / LeMaster, D.M. / Eklund, H.
#1: Journal: Proc.Natl.Acad.Sci.USA / Year: 1975
Title: Three-Dimensional Structure of Escherichia Coli Thioredoxin-S2 to 2.8 Angstroms Resolution
Authors: Holmgren, A. / Soderberg, B.-O. / Eklund, H. / Branden, C.-I.
#2: Journal: J.Mol.Biol. / Year: 1974
Title: Structure of Oxidized Thioredoxin to 4.5 Angstroms Resolution
Authors: Soderberg, B.-O. / Holmgren, A. / Branden, C.-I.
#3: Journal: J.Mol.Biol. / Year: 1970
Title: Crystallization and Preliminary Crystallographic Data for Thioredoxin from Escherichia Coli B
Authors: Holmgren, A. / Soderberg, B.-O.
History
DepositionMar 19, 1990Processing site: BNL
Revision 1.0Oct 15, 1991Provider: repository / Type: Initial release
Revision 1.1Mar 25, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / 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
Revision 1.4Nov 20, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_conn_angle / struct_conn / struct_site
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.ptnr1_symmetry / _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.ptnr1_symmetry / _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_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: THIOREDOXIN
B: THIOREDOXIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,32911
Polymers23,3752
Non-polymers9549
Water2,522140
1
A: THIOREDOXIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,2246
Polymers11,6871
Non-polymers5365
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: THIOREDOXIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,1055
Polymers11,6871
Non-polymers4184
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
A: THIOREDOXIN
hetero molecules

A: THIOREDOXIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,44712
Polymers23,3752
Non-polymers1,07210
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,y,-z1
Buried area3680 Å2
ΔGint-89 kcal/mol
Surface area10340 Å2
MethodPISA, PQS
4
B: THIOREDOXIN
hetero molecules

B: THIOREDOXIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,21110
Polymers23,3752
Non-polymers8368
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
MethodPQS
Unit cell
Length a, b, c (Å)89.500, 51.060, 60.450
Angle α, β, γ (deg.)90.00, 113.50, 90.00
Int Tables number5
Space group name H-MC121
Atom site foot note1: RESIDUES PRO A 76 AND PRO B 76 ARE CIS PROLINES.
2: RESIDUES HIS A 6, LEU A 7, ILE A 23, ASP A 47, GLU A 48, LEU A 58, LEU A 80, HIS B 6, ASP B 47, LEU B 58, AND LEU B 80 HAVE BEEN MODELED AS TWO CONFORMERS.
3: RESIDUES 11 - 21 IN CHAIN B ARE DISORDERED.

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Components

#1: Protein THIOREDOXIN


Mass: 11687.388 Da / Num. of mol.: 2
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


Mass: 63.546 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cu
#3: Chemical
ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 140 / 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

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Sample preparation

CrystalDensity Matthews: 2.71 Å3/Da / Density % sol: 54.58 %
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 3.8 / Method: microdialysis / Details: equilibrium dialysis
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
140 %(v/v)MPD1reservoir
20.01 Msodium acetate1reservior
31 mMcupric acetatae1reservoir

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Data collection

Reflection
*PLUS
Highest resolution: 1.68 Å / Lowest resolution: 2.5 Å / Num. obs: 27483 / Rmerge F obs: 0.063

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Processing

SoftwareName: PROFFT / Classification: refinement
RefinementResolution: 1.68→8 Å / σ(F): 3 /
RfactorNum. reflection
obs0.165 25969
Refinement stepCycle: LAST / Resolution: 1.68→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1644 0 58 140 1842
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0150.02
X-RAY DIFFRACTIONp_angle_d0.0350.03
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0550.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it1.381
X-RAY DIFFRACTIONp_mcangle_it2.281
X-RAY DIFFRACTIONp_scbond_it1.971
X-RAY DIFFRACTIONp_scangle_it3.271.5
X-RAY DIFFRACTIONp_plane_restr0.0210.02
X-RAY DIFFRACTIONp_chiral_restr0.1310.15
X-RAY DIFFRACTIONp_singtor_nbd0.1650.5
X-RAY DIFFRACTIONp_multtor_nbd0.1740.5
X-RAY DIFFRACTIONp_xhyhbond_nbd0.180.5
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor43
X-RAY DIFFRACTIONp_staggered_tor16.315
X-RAY DIFFRACTIONp_orthonormal_tor11.720
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor
Software
*PLUS
Name: PROFFT / Classification: refinement
Refinement
*PLUS
Num. reflection all: 26415 / Rfactor obs: 0.165
Solvent computation
*PLUS
Displacement parameters
*PLUS

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