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- PDB-1aba: THE STRUCTURE OF OXIDIZED BACTERIOPHAGE T4 GLUTAREDOXIN (THIOREDO... -

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Basic information

Entry
Database: PDB / ID: 1aba
TitleTHE STRUCTURE OF OXIDIZED BACTERIOPHAGE T4 GLUTAREDOXIN (THIOREDOXIN). REFINEMENT OF NATIVE AND MUTANT PROTEINS
ComponentsGLUTAREDOXIN
KeywordsELECTRON TRANSPORT
Function / homology
Function and homology information


deoxyribonucleotide biosynthetic process
Similarity search - Function
Glutaredoxin active site / Glutaredoxin active site. / Glutaredoxin / Glutaredoxin / Glutaredoxin domain profile. / Glutaredoxin / Glutaredoxin / Thioredoxin-like superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesEnterobacteria phage T4 (virus)
MethodX-RAY DIFFRACTION / Resolution: 1.45 Å
AuthorsEklund, H. / Ingelman, M. / Soderberg, B.-O. / Uhlin, T. / Nordlund, P. / Nikkola, M. / Sonnerstam, U. / Joelson, T. / Petratos, K.
Citation
Journal: J.Mol.Biol. / Year: 1992
Title: Structure of oxidized bacteriophage T4 glutaredoxin (thioredoxin). Refinement of native and mutant proteins.
Authors: Eklund, H. / Ingelman, M. / Soderberg, B.O. / Uhlin, T. / Nordlund, P. / Nikkola, M. / Sonnerstam, U. / Joelson, T. / Petratos, K.
#1: Journal: Proc.Natl.Acad.Sci.USA / Year: 1978
Title: Three-Dimensional Structure of Thioredoxin Induced by Bacteriophage T4
Authors: Soderberg, B.-O. / Sjoberg, B.-M. / Sonnerstam, U. / Branden, C.-I.
#2: Journal: J.Mol.Biol. / Year: 1976
Title: Thioredoxin Induced by Bacteriophage T4. Crystallization and Preliminary Crystallographic Data
Authors: Sjoberg, B.-M. / Soderberg, B.-O.
History
DepositionApr 24, 1992Processing site: BNL
Revision 1.0Oct 31, 1993Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jun 5, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / 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 / _pdbx_database_status.process_site / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 23, 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: GLUTAREDOXIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,1512
Polymers9,9551
Non-polymers1951
Water2,522140
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)30.200, 47.800, 61.300
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Atom site foot note1: RESIDUE PRO 66 IS A CIS PROLINE.

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Components

#1: Protein GLUTAREDOXIN


Mass: 9955.492 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacteria phage T4 (virus) / Genus: T4-like viruses / Species: Enterobacteria phage T4 sensu lato / References: UniProt: P00276
#2: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#3: 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: 2.22 Å3/Da / Density % sol: 44.62 %
Crystal grow
*PLUS
Temperature: 20 ℃ / pH: 6 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
15 %(w/v)PEG40001drop
225 mMMes1drop
315 mg/mlprotein1drop
410 %(w/v)PEG40001reservoirs
550 mMMes1reservoir

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 1.45 Å / Num. obs: 15227 / % possible obs: 92 % / Rmerge(I) obs: 0.052

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
RefinementRfactor Rwork: 0.175 / Rfactor obs: 0.175 / Highest resolution: 1.45 Å
Refinement stepCycle: LAST / Highest resolution: 1.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms728 0 12 140 880
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.012
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_deg2.53
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
Refinement
*PLUS
Highest resolution: 1.45 Å / Rfactor obs: 0.175
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_angle_d2.53
X-RAY DIFFRACTIONx_dihedral_angle_d24.5
X-RAY DIFFRACTIONx_dihedral_angle_deg

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