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- PDB-1fb0: CRYSTAL STRUCTURE OF THIOREDOXIN M FROM SPINACH CHLOROPLAST (REDU... -

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Basic information

Entry
Database: PDB / ID: 1fb0
TitleCRYSTAL STRUCTURE OF THIOREDOXIN M FROM SPINACH CHLOROPLAST (REDUCED FORM)
ComponentsTHIOREDOXIN M
KeywordsELECTRON TRANSPORT
Function / homology
Function and homology information


protein-disulfide reductase activity / enzyme activator activity / chloroplast
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
Thioredoxin M-type, chloroplastic
Similarity search - Component
Biological speciesSpinacia oleracea (spinach)
MethodX-RAY DIFFRACTION / Resolution: 2.26 Å
AuthorsCapitani, G. / Markovic-Housley, Z. / DelVal, G. / Morris, M. / Jansonius, J.N. / Schurmann, P.
CitationJournal: J.Mol.Biol. / Year: 2000
Title: Crystal structures of two functionally different thioredoxins in spinach chloroplasts.
Authors: Capitani, G. / Markovic-Housley, Z. / DelVal, G. / Morris, M. / Jansonius, J.N. / Schurmann, P.
History
DepositionJul 14, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 20, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: THIOREDOXIN M
B: THIOREDOXIN M


Theoretical massNumber of molelcules
Total (without water)23,5872
Polymers23,5872
Non-polymers00
Water2,036113
1
A: THIOREDOXIN M


Theoretical massNumber of molelcules
Total (without water)11,7931
Polymers11,7931
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: THIOREDOXIN M


Theoretical massNumber of molelcules
Total (without water)11,7931
Polymers11,7931
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)74.600, 74.600, 74.260
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
DetailsThe biological assembly is a monomer

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Components

#1: Protein THIOREDOXIN M


Mass: 11793.436 Da / Num. of mol.: 2 / Fragment: REDUCED FORM
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Spinacia oleracea (spinach) / Cellular location: CHLOROPLAST / Plasmid: PKK233-2 (MODIFIED) / Production host: Escherichia coli (E. coli) / References: UniProt: P07591
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 113 / Source method: isolated from a natural source / Formula: H2O
Compound detailsActive site disulphide bridge is in reduced form (obtained through a DTT soak).

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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: 2.53 Å3/Da / Density % sol: 51.33 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: sodium acetate, PEG monomethylether 2000, ammonium sulphate , pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
Temperature: 20 ℃ / pH: 7.3
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
150 mg/mlprotein1drop
250 mMTris-HCl1drop
30.02 %(w/v)1dropNaN3
40.2 Mammonium sulfate1reservoir
50.1 Msodium acetate1reservoir
630 %(w/v)PEG2000 mme1reservoir

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Data collection

DiffractionMean temperature: 277 K
Diffraction sourceSource: ROTATING ANODE / Type: ELLIOTT GX-20 / Wavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Apr 12, 1997
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.26→26.4 Å / Num. obs: 10890 / % possible obs: 94.3 % / Observed criterion σ(I): -3 / Redundancy: 1.9 % / Biso Wilson estimate: 28.6 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 10
Reflection shellResolution: 2.26→2.31 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.269 / % possible all: 91.7
Reflection
*PLUS
Rmerge(I) obs: 0.07
Reflection shell
*PLUS
% possible obs: 91.7 %

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Processing

Software
NameVersionClassification
AMoREphasing
X-PLOR3.851refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementResolution: 2.26→26.4 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
Details: Used overall anisotropic B-factor refinement and bulk solvent correction (X-PLOR 3.851 and CNS)
RfactorNum. reflection% reflectionSelection details
Rfree0.235 593 -RANDOM
Rwork0.198 ---
obs-10890 94.3 %-
Refinement stepCycle: LAST / Resolution: 2.26→26.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1653 0 0 113 1766
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.006
X-RAY DIFFRACTIONx_angle_deg1.1
X-RAY DIFFRACTIONx_dihedral_angle_d23.6
X-RAY DIFFRACTIONx_improper_angle_d0.75
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 26.4 Å / σ(F): 0 / % reflection Rfree: 5.4 % / Rfactor obs: 0.198
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 22.2 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_angle_deg1.1
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg23.6
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg0.75

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