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- PDB-2fls: Crystal structure of Human Glutaredoxin 2 complexed with glutathione -

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Basic information

Entry
Database: PDB / ID: 2fls
TitleCrystal structure of Human Glutaredoxin 2 complexed with glutathione
ComponentsGlutaredoxin-2
KeywordsOXIDOREDUCTASE / Thioredoxin fold / Structural Genomics / Structural Genomics Consortium / SGC
Function / homology
Function and homology information


cellular response to superoxide / arsenate reductase (glutaredoxin) activity / glutathione disulfide oxidoreductase activity / DNA protection / response to redox state / response to temperature stimulus / protein disulfide isomerase activity / protein-disulfide reductase activity / regulation of signal transduction / glutathione metabolic process ...cellular response to superoxide / arsenate reductase (glutaredoxin) activity / glutathione disulfide oxidoreductase activity / DNA protection / response to redox state / response to temperature stimulus / protein disulfide isomerase activity / protein-disulfide reductase activity / regulation of signal transduction / glutathione metabolic process / : / cell redox homeostasis / response to hydrogen peroxide / 2 iron, 2 sulfur cluster binding / electron transfer activity / cell differentiation / mitochondrial matrix / intracellular membrane-bounded organelle / neuronal cell body / apoptotic process / dendrite / regulation of DNA-templated transcription / mitochondrion / nucleoplasm / nucleus / metal ion binding
Similarity search - Function
Glutaredoxin subgroup / Glutaredoxin, eukaryotic/virial / Glutaredoxin / Glutaredoxin / Glutaredoxin domain profile. / Glutaredoxin / Glutaredoxin / Thioredoxin-like superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
GLUTATHIONE / Glutaredoxin-2, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 Å
AuthorsJohansson, C. / Smee, C. / Kavanagh, K.L. / Debreczeni, J. / von Delft, F. / Gileadi, O. / Arrowsmith, C. / Weigelt, J. / Edwards, A. / Sundstrom, M. ...Johansson, C. / Smee, C. / Kavanagh, K.L. / Debreczeni, J. / von Delft, F. / Gileadi, O. / Arrowsmith, C. / Weigelt, J. / Edwards, A. / Sundstrom, M. / Oppermann, U. / Structural Genomics Consortium (SGC)
CitationJournal: To be Published
Title: Crystal structure of Human Glutaredoxin 2 complexed with glutathione
Authors: Johansson, C. / Smee, C. / Kavanagh, K.L. / Debreczeni, J. / Oppermann, U. / Sundstrom, M.
History
DepositionJan 6, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 24, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Dec 5, 2012Group: Other
Revision 1.4Jan 31, 2018Group: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.5Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,6072
Polymers15,3001
Non-polymers3071
Water95553
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)60.201, 60.201, 67.958
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein Glutaredoxin-2


Mass: 15299.536 Da / Num. of mol.: 1 / Fragment: residues 56-164
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GLRX2, GRX2 / Plasmid: pET28 derived, pNIC28-BSA4 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q9NS18
#2: Chemical ChemComp-GSH / GLUTATHIONE


Mass: 307.323 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17N3O6S
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 53 / Source method: isolated from a natural source / Formula: H2O

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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: 2.32 Å3/Da / Density % sol: 47.05 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 3.5
Details: 0.1 M citrate, 25% PEG 3350, pH 3.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.9184 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Dec 9, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 2.05→41.38 Å / Num. all: 9322 / Num. obs: 9322 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.9 % / Biso Wilson estimate: 29 Å2 / Rmerge(I) obs: 0.115 / Net I/σ(I): 13.5
Reflection shellResolution: 2.05→2.16 Å / Redundancy: 5.8 % / Mean I/σ(I) obs: 2.5 / Num. unique all: 7834 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2CQ9

2cq9


Resolution: 2.05→41.38 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.938 / SU B: 8.222 / SU ML: 0.113 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.164 / ESU R Free: 0.154 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. The dataset was analyzed for twinning and showed a twin fraction of ~20%. Consequently, the dataset was processed using the program DETWIN ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. The dataset was analyzed for twinning and showed a twin fraction of ~20%. Consequently, the dataset was processed using the program DETWIN and refinement finalized with the detwinned data
RfactorNum. reflection% reflectionSelection details
Rfree0.2309 448 5 %RANDOM
Rwork0.19045 ---
all0.192 8589 --
obs0.19238 8589 97.11 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 23.02 Å2
Baniso -1Baniso -2Baniso -3
1-0.87 Å20.43 Å20 Å2
2--0.87 Å20 Å2
3----1.3 Å2
Refinement stepCycle: LAST / Resolution: 2.05→41.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms784 0 20 53 857
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.022820
X-RAY DIFFRACTIONr_bond_other_d0.0010.02525
X-RAY DIFFRACTIONr_angle_refined_deg1.5021.9641112
X-RAY DIFFRACTIONr_angle_other_deg1.0053.0031285
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5435100
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.60124.44436
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.07415130
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.745153
X-RAY DIFFRACTIONr_chiral_restr0.0820.2128
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02911
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02162
X-RAY DIFFRACTIONr_nbd_refined0.190.2155
X-RAY DIFFRACTIONr_nbd_other0.1860.2505
X-RAY DIFFRACTIONr_nbtor_refined0.1730.2399
X-RAY DIFFRACTIONr_nbtor_other0.0880.2405
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1710.233
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_other0.3720.210
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1420.23
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.7543518
X-RAY DIFFRACTIONr_mcbond_other0.753204
X-RAY DIFFRACTIONr_mcangle_it3.7775810
X-RAY DIFFRACTIONr_scbond_it6.237341
X-RAY DIFFRACTIONr_scangle_it7.23711302
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.05→2.103 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.389 32 -
Rwork0.247 622 -
obs--96.46 %
Refinement TLS params.Method: refined / Origin x: -25.9147 Å / Origin y: 16.0469 Å / Origin z: 7.7576 Å
111213212223313233
T-0.0349 Å2-0.004 Å20.0068 Å2--0.1301 Å2-0.0108 Å2---0.1242 Å2
L3.3578 °21.2874 °2-0.787 °2-3.1792 °2-1.2134 °2--3.8999 °2
S-0.0999 Å °-0.1388 Å °0.1668 Å °0.0879 Å °0.0624 Å °0.1116 Å °-0.1218 Å °0.1515 Å °0.0375 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA15 - 11523 - 123
2X-RAY DIFFRACTION1AB125

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