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- PDB-2wz9: Crystal structure of the thioredoxin domain of human TXNL2 -

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Basic information

Entry
Database: PDB / ID: 2wz9
TitleCrystal structure of the thioredoxin domain of human TXNL2
ComponentsGLUTAREDOXIN-3
KeywordsPROTEIN BINDING
Function / homology
Function and homology information


protein maturation by iron-sulfur cluster transfer / negative regulation of cardiac muscle hypertrophy / regulation of the force of heart contraction / iron-sulfur cluster assembly complex / [2Fe-2S] cluster assembly / iron-sulfur cluster assembly / iron-sulfur cluster binding / cell redox homeostasis / Iron uptake and transport / protein kinase C binding ...protein maturation by iron-sulfur cluster transfer / negative regulation of cardiac muscle hypertrophy / regulation of the force of heart contraction / iron-sulfur cluster assembly complex / [2Fe-2S] cluster assembly / iron-sulfur cluster assembly / iron-sulfur cluster binding / cell redox homeostasis / Iron uptake and transport / protein kinase C binding / Z disc / cell cortex / intracellular iron ion homeostasis / dendrite / RNA binding / identical protein binding / nucleus / metal ion binding / cytosol / cytoplasm
Similarity search - Function
Monothiol glutaredoxin-related / Glutaredoxin, PICOT-like / Glutaredoxin / Glutaredoxin / Glutaredoxin domain profile. / Thioredoxin / Thioredoxin domain profile. / Thioredoxin domain / Glutaredoxin / Glutaredoxin ...Monothiol glutaredoxin-related / Glutaredoxin, PICOT-like / Glutaredoxin / Glutaredoxin / Glutaredoxin domain profile. / Thioredoxin / Thioredoxin domain profile. / Thioredoxin domain / Glutaredoxin / Glutaredoxin / Thioredoxin-like superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 Å
AuthorsVollmar, M. / Johannson, C. / Cocking, R. / Pike, A.C.W. / Muniz, J.R.C. / Edwards, A. / von Delft, F. / Bountra, C. / Arrowsmith, C.H. / Weigelt, J. / Kavanagh, K.L.
CitationJournal: To be Published
Title: Crystal Structure of the Thioredoxin Domain of Human Txnl2
Authors: Vollmar, M. / Johannson, C. / Cocking, R. / Pike, A.C.W. / Muniz, J.R.C. / Edwards, A. / von Delft, F. / Bountra, C. / Kavanagh, K.L.
History
DepositionNov 25, 2009Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 16, 2010Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 24, 2018Group: Database references / Structure summary / Category: audit_author / citation_author / Item: _audit_author.name / _citation_author.name
Revision 1.4Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: GLUTAREDOXIN-3


Theoretical massNumber of molelcules
Total (without water)16,6301
Polymers16,6301
Non-polymers00
Water2,558142
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)42.630, 52.060, 58.600
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein GLUTAREDOXIN-3 / THIOREDOXIN-LIKE PROTEIN 2 / PKC-INTERACTING COUSIN OF THIOREDOXIN / PKC-THETA-INTERACTING PROTEIN ...THIOREDOXIN-LIKE PROTEIN 2 / PKC-INTERACTING COUSIN OF THIOREDOXIN / PKC-THETA-INTERACTING PROTEIN / PKCQ- INTERACTING PROTEIN


Mass: 16629.838 Da / Num. of mol.: 1 / Fragment: THIOREDOXIN DOMAIN, RESIDUES 2-125
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PNIC28-BSA4 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): R3-PRARE2 / References: UniProt: O76003
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 142 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsSEQUENCE TOWARDS C TERMINUS CARRIES SEVEN MUTATIONS INTRODUCED BY PCR

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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: 2.21 Å3/Da / Density % sol: 44.49 % / Description: NONE
Crystal growDetails: 1.4 M AMMONIUM CITRATE, PH 7

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9796
DetectorType: ADSC CCD / Detector: CCD / Date: Sep 25, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9796 Å / Relative weight: 1
ReflectionResolution: 1.55→34.47 Å / Num. obs: 19534 / % possible obs: 99.8 % / Observed criterion σ(I): 0 / Redundancy: 3.8 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 9.5
Reflection shellResolution: 1.55→1.63 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.58 / Mean I/σ(I) obs: 2.2 / % possible all: 99.6

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Processing

Software
NameVersionClassification
REFMAC5.5.0089refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2DIY

2diy


Resolution: 1.55→58.6 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.964 / SU B: 1.253 / SU ML: 0.044 / Cross valid method: THROUGHOUT / ESU R: 0.068 / ESU R Free: 0.069 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.179 986 5 %RANDOM
Rwork0.154 ---
obs0.156 18548 99.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 12.37 Å2
Baniso -1Baniso -2Baniso -3
1--0.13 Å20 Å20 Å2
2--0.61 Å20 Å2
3----0.48 Å2
Refinement stepCycle: LAST / Resolution: 1.55→58.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms925 0 0 142 1067
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.022994
X-RAY DIFFRACTIONr_bond_other_d0.0010.02681
X-RAY DIFFRACTIONr_angle_refined_deg1.5781.9661344
X-RAY DIFFRACTIONr_angle_other_deg2.39431694
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.95121
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.85825.43546
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.32315188
X-RAY DIFFRACTIONr_dihedral_angle_4_deg28.51154
X-RAY DIFFRACTIONr_chiral_restr0.0970.2150
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0211078
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02184
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.463608
X-RAY DIFFRACTIONr_mcbond_other0.7433238
X-RAY DIFFRACTIONr_mcangle_it4.3775991
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it7.3778386
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it10.02712352
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr3.4631665
X-RAY DIFFRACTIONr_sphericity_free14.0833142
X-RAY DIFFRACTIONr_sphericity_bonded5.66431643
LS refinement shellResolution: 1.55→1.59 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.27 72 -
Rwork0.273 1356 -
obs--99.03 %

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