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- PDB-1ep8: CRYSTAL STRUCTURE OF A MUTATED THIOREDOXIN, D30A, FROM CHLAMYDOMO... -

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Basic information

Entry
Database: PDB / ID: 1ep8
TitleCRYSTAL STRUCTURE OF A MUTATED THIOREDOXIN, D30A, FROM CHLAMYDOMONAS REINHARDTII
ComponentsTHIOREDOXIN CH1, H-TYPE
KeywordsELECTRON TRANSPORT / mutant
Function / homology
Function and homology information


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
Biological speciesChlamydomonas reinhardtii (plant)
MethodX-RAY DIFFRACTION / Resolution: 2.2 Å
AuthorsMenchise, V. / Corbier, C. / Didierjean, C. / Saviano, M. / Benedetti, E. / Jacquot, J.P. / Aubry, A.
Citation
Journal: Biochem.J. / Year: 2001
Title: Crystal structure of the wild-type and D30A mutant thioredoxin h of Chlamydomonas reinhardtii and implications for the catalytic mechanism.
Authors: Menchise, V. / Corbier, C. / Didierjean, C. / Saviano, M. / Benedetti, E. / Jacquot, J.P. / Aubry, A.
#1: Journal: Eur.J.Biochem. / Year: 1997
Title: NMR Solution Structure of an Oxidized Thioredoxin h from the Eukaryotic Green alga Chlamydomonas reinhardtii
Authors: Mittard, V. / Blackledge, M.J. / Stein, M. / Jacquot, J. / Marion, D. / Lancelin, J.M.
History
DepositionMar 28, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 12, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 3, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Nov 20, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / 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 CH1, H-TYPE
B: THIOREDOXIN CH1, H-TYPE


Theoretical massNumber of molelcules
Total (without water)23,3672
Polymers23,3672
Non-polymers00
Water79344
1
A: THIOREDOXIN CH1, H-TYPE


Theoretical massNumber of molelcules
Total (without water)11,6841
Polymers11,6841
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: THIOREDOXIN CH1, H-TYPE


Theoretical massNumber of molelcules
Total (without water)11,6841
Polymers11,6841
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)49.692, 49.692, 145.551
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein THIOREDOXIN CH1, H-TYPE


Mass: 11683.524 Da / Num. of mol.: 2 / Mutation: D30A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chlamydomonas reinhardtii (plant) / Production host: Escherichia coli (E. coli) / References: UniProt: P80028
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 44 / 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: 2.22 Å3/Da / Density % sol: 44.58 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: PEG 8000, PEG 10000, Cacodylate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
118 mg/mlprotein1drop
210 %(w/v)PEG80001reservoir
310 %(w/v)PEG100001reservoir
40.1 Msodium cacodylate1reservoirpH6.5

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: ENRAF-NONIUS FR591 / Wavelength: 1.5418
DetectorType: MACSCIENCE / Detector: IMAGE PLATE / Date: Jun 4, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.2→20 Å / Num. all: 53351 / Num. obs: 10823 / % possible obs: 96.4 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 5 % / Rmerge(I) obs: 0.047 / Net I/σ(I): 26.8
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 4 % / Rmerge(I) obs: 0.17 / Num. unique all: 1006 / % possible all: 91.6
Reflection
*PLUS
Num. measured all: 53351
Reflection shell
*PLUS
% possible obs: 91.6 % / Mean I/σ(I) obs: 6.2

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNS0.9refinement
RefinementResolution: 2.2→20 Å / σ(F): 0 / σ(I): 0
Details: The two molecules, A and B, have been refined independently, without imposing non-crystallographic 2-fold axis.
RfactorNum. reflectionSelection details
Rfree0.22 1114 random
Rwork0.196 --
all-10823 -
obs-10823 -
Refinement stepCycle: LAST / Resolution: 2.2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1642 0 0 44 1686
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.018
X-RAY DIFFRACTIONc_angle_deg1.68
X-RAY DIFFRACTIONc_dihedral_angle_d24.9
Software
*PLUS
Name: CNS / Version: 0.9 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 20 Å / σ(F): 0 / Rfactor obs: 0.196 / Rfactor Rfree: 0.22
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg24.9

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