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- PDB-1f9m: CRYSTAL STRUCTURE OF THIOREDOXIN F FROM SPINACH CHLOROPLAST (SHOR... -

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Basic information

Entry
Database: PDB / ID: 1f9m
TitleCRYSTAL STRUCTURE OF THIOREDOXIN F FROM SPINACH CHLOROPLAST (SHORT FORM)
ComponentsTHIOREDOXIN F
KeywordsELECTRON TRANSPORT
Function / homology
Function and homology information


protein-disulfide reductase activity / chloroplast / cytosol
Similarity search - Function
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 F-type, chloroplastic
Similarity search - Component
Biological speciesSpinacia oleracea (spinach)
MethodX-RAY DIFFRACTION / Resolution: 1.86 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 11, 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 1.3Oct 30, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
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 F
B: THIOREDOXIN F


Theoretical massNumber of molelcules
Total (without water)25,0152
Polymers25,0152
Non-polymers00
Water2,558142
1
A: THIOREDOXIN F


Theoretical massNumber of molelcules
Total (without water)12,5081
Polymers12,5081
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: THIOREDOXIN F


Theoretical massNumber of molelcules
Total (without water)12,5081
Polymers12,5081
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)46.59, 52.56, 52.57
Angle α, β, γ (deg.)90.0, 108.93, 90.0
Int Tables number4
Space group name H-MP1211
DetailsThe biological assembly is a monomer

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Components

#1: Protein THIOREDOXIN F


Mass: 12507.648 Da / Num. of mol.: 2 / Fragment: SHORT FORM
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Spinacia oleracea (spinach) / Cellular location: CHLOROPLAST / Plasmid: PET-3D / Production host: Escherichia coli (E. coli) / References: UniProt: P09856
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 142 / 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: 2.43 Å3/Da / Density % sol: 49.44 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.8
Details: ammonium sulphate, sodium acetate, PEG 4000, pH 5.80, 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
130 mg/mlprotein1drop
250 mMTris-HCl1drop
30.2 M1dropNaCl
40.02 %(w/v)1dropNaN3
50.2 Mammonium sulfate1reservoir
60.1 Msodium acetate1reservoir
725 %(w/v)PEG40001reservoir

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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: Oct 2, 1995
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.86→25.5 Å / Num. obs: 20015 / % possible obs: 98.9 % / Redundancy: 2.9 % / Biso Wilson estimate: 19.8 Å2 / Rmerge(I) obs: 0.082 / Net I/σ(I): 5.7
Reflection shellResolution: 1.86→1.96 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.237 / % possible all: 95.3

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
PHASESphasing
X-PLOR3.851refinement
CCP4(SCALA)data scaling
RefinementResolution: 1.86→25.5 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: Used bulk solvent correction (X-PLOR 3.851)
RfactorNum. reflection% reflectionSelection details
Rfree0.237 967 -RANDOM
Rwork0.198 ---
obs-20015 98.9 %-
Refinement stepCycle: LAST / Resolution: 1.86→25.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1752 0 0 142 1894
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.01
X-RAY DIFFRACTIONx_angle_deg1.3
X-RAY DIFFRACTIONx_dihedral_angle_d25.8
X-RAY DIFFRACTIONx_improper_angle_d0.81
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 25.5 Å / σ(F): 0 / % reflection Rfree: 4.8 % / Rfactor obs: 0.197
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 22.3 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.01
X-RAY DIFFRACTIONx_angle_deg1.3
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg25.8
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg0.81

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