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- PDB-1faa: CRYSTAL STRUCTURE OF THIOREDOXIN F FROM SPINACH CHLOROPLAST (LONG... -

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Basic information

Entry
Database: PDB / ID: 1faa
TitleCRYSTAL STRUCTURE OF THIOREDOXIN F FROM SPINACH CHLOROPLAST (LONG 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: 1.85 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 13, 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 4, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Apr 18, 2018Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.detector
Revision 1.5Nov 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 1.6Oct 16, 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 F


Theoretical massNumber of molelcules
Total (without water)13,9201
Polymers13,9201
Non-polymers00
Water61334
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)30.6, 63.1, 31.6
Angle α, β, γ (deg.)90.00, 110.7, 90.00
Int Tables number4
Space group name H-MP1211
DetailsThe biological assembly is a monomer

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Components

#1: Protein THIOREDOXIN F


Mass: 13920.255 Da / Num. of mol.: 1 / Fragment: LONG FORM / Mutation: M1L, Q3L
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: P09856
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 34 / 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: 2.05 Å3/Da / Density % sol: 39.98 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: sodium acetate, 2,5-hexane diol, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
Details: Genovesio-Taverne, J.C., (1991) J. Mol. Biol., 222, 459.

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: ROTATING ANODE / Type: ENRAF-NONIUS FR571 / Wavelength: 1.5418
DetectorType: ENRAF-NONIUS FAST / Detector: DIFFRACTOMETER / Date: 1991
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.85→25.6 Å / Num. obs: 9180 / % possible obs: 95.2 % / Biso Wilson estimate: 25.6 Å2 / Rmerge(I) obs: 0.035

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Processing

Software
NameVersionClassification
MADNESSdata collection
ROTAVATAdata reduction
AMoREphasing
X-PLOR3.851refinement
MADNESSdata reduction
CCP4(AGROVATAdata scaling
ROTAVATAdata scaling
RefinementResolution: 1.85→25.6 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
Details: Used overall anisotropic B-factor refinement and bulk solvent correction (X-PLOR 3.851)
RfactorNum. reflection% reflectionSelection details
Rfree0.268 299 -RANDOM
Rwork0.209 ---
obs-9180 95.2 %-
Refinement stepCycle: LAST / Resolution: 1.85→25.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms943 0 0 34 977
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.01
X-RAY DIFFRACTIONx_angle_deg1.3
X-RAY DIFFRACTIONx_dihedral_angle_d26.7
X-RAY DIFFRACTIONx_improper_angle_d0.73
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 25.6 Å / σ(F): 0 / % reflection Rfree: 3.1 % / Rfactor obs: 0.209
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 34.2 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_deg26.7
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg0.73

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