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- PDB-2yan: Crystal structure of the second glutaredoxin domain of human TXNL2 -

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Basic information

Entry
Database: PDB / ID: 2yan
TitleCrystal structure of the second glutaredoxin domain of human TXNL2
ComponentsGLUTAREDOXIN-3
KeywordsOXIDOREDUCTASE
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
: / GLUTATHIONE / Glutaredoxin-3
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsVollmar, M. / Johansson, C. / Cocking, R. / Muniz, J.R.C. / Krojer, T. / Allerston, C. / von Delft, F. / Bountra, C. / Arrowsmith, C.H. / Weigelt, J. ...Vollmar, M. / Johansson, C. / Cocking, R. / Muniz, J.R.C. / Krojer, T. / Allerston, C. / von Delft, F. / Bountra, C. / Arrowsmith, C.H. / Weigelt, J. / Edwards, A. / Oppermann, U.
CitationJournal: To be Published
Title: Crystal Structure of the Second Glutaredoxin Domain of Human Txnl2
Authors: Vollmar, M. / Johansson, C. / Cocking, R. / Muniz, J.R.C. / Krojer, T. / Allerston, C. / von Delft, F. / Bountra, C. / Arrowsmith, C.H. / Weigelt, J. / Edwards, A. / Oppermann, U.
History
DepositionFeb 23, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 30, 2011Provider: repository / Type: Initial release
Revision 1.1Jan 18, 2012Group: Other
Revision 1.2Dec 5, 2012Group: Database references
Revision 1.3Jan 24, 2018Group: Database references / Category: citation_author / Item: _citation_author.name
Revision 1.4Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / 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 / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: GLUTAREDOXIN-3
B: GLUTAREDOXIN-3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,05014
Polymers23,8132
Non-polymers1,23612
Water3,549197
1
A: GLUTAREDOXIN-3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,6509
Polymers11,9071
Non-polymers7438
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: GLUTAREDOXIN-3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,4005
Polymers11,9071
Non-polymers4944
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)118.317, 118.317, 58.840
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein GLUTAREDOXIN-3


Mass: 11906.729 Da / Num. of mol.: 2 / Fragment: GLUTAREDOXIN DOMAIN, RESIDUES 232-334
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

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Non-polymers , 6 types, 209 molecules

#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Chemical ChemComp-GSH / GLUTATHIONE


Mass: 307.323 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H17N3O6S
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 197 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsSEQUENCE START S230 AND MET231 DUE TO CLONING STRATEGY.

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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: 4.99 Å3/Da / Density % sol: 72.31 % / Description: NONE
Crystal growDetails: 0.1 M ACETATE PH 4.5, 2 M(NH4)2 SO4.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 1
DetectorType: ADSC CCD / Detector: CCD / Date: Jan 15, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→19.72 Å / Num. obs: 37552 / % possible obs: 99.8 % / Observed criterion σ(I): 2 / Redundancy: 6.1 % / Biso Wilson estimate: 33.8 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 11.7
Reflection shellResolution: 1.9→2 Å / Redundancy: 6.2 % / Rmerge(I) obs: 0.82 / Mean I/σ(I) obs: 2 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.5.0110refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRIES 1WIK, 2WCI, 2WUL, 2WZ9, 3IPZ ENSEMBLE

1wik

2wci

2wul

2wz9

3ipz


Resolution: 1.9→19.72 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.949 / SU B: 4.093 / SU ML: 0.066 / Cross valid method: THROUGHOUT / ESU R: 0.097 / ESU R Free: 0.098 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.21237 1872 5 %RANDOM
Rwork0.18491 ---
obs0.18629 35624 99.79 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 30.092 Å2
Baniso -1Baniso -2Baniso -3
1-0.91 Å20.46 Å20 Å2
2--0.91 Å20 Å2
3----1.37 Å2
Refinement stepCycle: LAST / Resolution: 1.9→19.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1664 0 75 197 1936
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0221849
X-RAY DIFFRACTIONr_bond_other_d0.0010.021321
X-RAY DIFFRACTIONr_angle_refined_deg1.4842.042493
X-RAY DIFFRACTIONr_angle_other_deg0.8793.0013273
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.0665239
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.44626.34182
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.59915368
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.729157
X-RAY DIFFRACTIONr_chiral_restr0.0880.2277
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022005
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02316
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_it0.8631.51086
X-RAY DIFFRACTIONr_mcbond_other0.2381.5444
X-RAY DIFFRACTIONr_mcangle_it1.49621763
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.293763
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.7624.5714
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.353 139 -
Rwork0.338 2586 -
obs--100 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
14.327-1.60832.111619.2708-14.267110.77160.1765-0.0980.64970.1591-0.10320.2923-0.08980.0254-0.07320.2696-0.1408-0.05570.1967-0.0110.210442.8197-22.02921.4553
23.0480.79050.18353.0313-0.12163.43080.1607-0.09450.290.3484-0.23040.2533-0.2325-0.01490.06970.1102-0.1015-0.00610.1631-0.01740.119834.3091-34.582123.5189
33.19523.95544.575924.73265.606916.33770.44630.093-0.59760.95220.0129-1.45120.74610.9744-0.45920.17550.0206-0.06360.30950.06660.256244.7673-47.077825.1781
43.46525.39966.97988.685613.421338.4237-0.33470.07480.2372-0.48870.08110.3244-0.50880.21260.25360.2286-0.0347-0.06330.26640.05720.171543.9555-39.2183-11.1806
51.8673-0.3596-1.20861.84761.51776.4498-0.01640.1525-0.0872-0.2377-0.00620.02840.1287-0.0820.02250.0629-0.0378-0.03240.2101-0.00110.124642.2186-44.03882.6536
614.65560.00610.503111.27591.53465.9559-0.0128-0.28850.16860.25330.1475-0.1726-0.13740.3757-0.13470.0149-0.01190.02040.3098-0.08210.121655.0058-42.245210.4854
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A230 - 248
2X-RAY DIFFRACTION2A249 - 320
3X-RAY DIFFRACTION3A321 - 333
4X-RAY DIFFRACTION4B230 - 248
5X-RAY DIFFRACTION5B249 - 314
6X-RAY DIFFRACTION6B315 - 333

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