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- PDB-3zyw: Crystal structure of the first glutaredoxin domain of human gluta... -

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Basic information

Entry
Database: PDB / ID: 3zyw
TitleCrystal structure of the first glutaredoxin domain of human glutaredoxin 3 (GLRX3)
ComponentsGLUTAREDOXIN-3
KeywordsMETAL BINDING PROTEIN
Function / homology
Function and homology information


protein maturation by iron-sulfur cluster transfer / negative regulation of cardiac muscle hypertrophy / iron-sulfur cluster assembly complex / regulation of the force of heart contraction / [2Fe-2S] cluster assembly / iron-sulfur cluster assembly / iron-sulfur cluster binding / cell redox homeostasis / protein kinase C binding / Iron uptake and transport ...protein maturation by iron-sulfur cluster transfer / negative regulation of cardiac muscle hypertrophy / iron-sulfur cluster assembly complex / regulation of the force of heart contraction / [2Fe-2S] cluster assembly / iron-sulfur cluster assembly / iron-sulfur cluster binding / cell redox homeostasis / protein kinase C binding / Iron uptake and transport / Z disc / cell cortex / intracellular iron ion homeostasis / dendrite / RNA binding / identical protein binding / metal ion binding / nucleus / 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: 1.84 Å
AuthorsVollmar, M. / Johansson, C. / Cocking, R. / Krojer, T. / Muniz, J.R.C. / Kavanagh, K.L. / von Delft, F. / Bountra, C. / Arrowsmith, C.H. / Weigelt, J. ...Vollmar, M. / Johansson, C. / Cocking, R. / Krojer, T. / Muniz, J.R.C. / Kavanagh, K.L. / von Delft, F. / Bountra, C. / Arrowsmith, C.H. / Weigelt, J. / Edwards, A. / Oppermann, U.
CitationJournal: To be Published
Title: Crystal Structure of the First Glutaredoxin Domain of Human Glutaredoxin 3 (Glrx3)
Authors: Vollmar, M. / Johansson, C. / Cocking, R. / Krojer, T. / Muniz, J.R.C. / Kavanagh, K.L. / von Delft, F. / Bountra, C. / Arrowsmith, C.H. / Weigelt, J. / Edwards, A. / Oppermann, U.
History
DepositionAug 29, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 29, 2012Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2018Group: Database references / Structure summary / Category: audit_author / citation_author / Item: _audit_author.name / _citation_author.name
Revision 1.2Dec 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_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_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)25,7967
Polymers25,4852
Non-polymers3105
Water7,386410
1
A: GLUTAREDOXIN-3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,8673
Polymers12,7431
Non-polymers1242
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: GLUTAREDOXIN-3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,9294
Polymers12,7431
Non-polymers1863
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)34.524, 87.052, 90.705
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP22121

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Components

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


Mass: 12742.636 Da / Num. of mol.: 2 / Fragment: GLUTAREDOXIN DOMAIN, RESIDUES 130-232
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PNIC-CTHF / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): R3-PRARE2 / References: UniProt: O76003
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 410 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsSTARTING MET0 IN CHAIN B AS WELL AS TERMINAL RESIDUES ALA233 GLU234 ASN235 LEU236 TYR237 PHE238 ...STARTING MET0 IN CHAIN B AS WELL AS TERMINAL RESIDUES ALA233 GLU234 ASN235 LEU236 TYR237 PHE238 GLN239 ARE DUE TO CONSTRUCT DESIGN

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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: 2.69 Å3/Da / Density % sol: 54.22 % / Description: NONE
Crystal growDetails: 0.1M BIS-TRIS PH 5.5, 25% PEG3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 4, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.84→19.62 Å / Num. obs: 23870 / % possible obs: 97.8 % / Observed criterion σ(I): 2.6 / Redundancy: 6.3 % / Biso Wilson estimate: 17.1 Å2 / Rmerge(I) obs: 0.13 / Net I/σ(I): 11.4
Reflection shellResolution: 1.84→1.94 Å / Redundancy: 6 % / Rmerge(I) obs: 0.7 / Mean I/σ(I) obs: 2.6 / % possible all: 88.3

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Processing

Software
NameVersionClassification
REFMAC5.6.0117refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2YAN

2yan


Resolution: 1.84→18.95 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.91 / SU B: 3.773 / SU ML: 0.112 / Cross valid method: THROUGHOUT / ESU R: 0.153 / ESU R Free: 0.149 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY.
RfactorNum. reflection% reflectionSelection details
Rfree0.24974 1215 5.1 %RANDOM
Rwork0.19975 ---
obs0.20241 22530 97.22 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 14.264 Å2
Baniso -1Baniso -2Baniso -3
1--1.71 Å20 Å20 Å2
2--2.62 Å20 Å2
3----0.91 Å2
Refinement stepCycle: LAST / Resolution: 1.84→18.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1757 0 20 410 2187
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0221872
X-RAY DIFFRACTIONr_bond_other_d0.0010.021321
X-RAY DIFFRACTIONr_angle_refined_deg1.3821.9852529
X-RAY DIFFRACTIONr_angle_other_deg0.87233253
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5875237
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.79725.45588
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.51215350
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.93156
X-RAY DIFFRACTIONr_chiral_restr0.0920.2271
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0212059
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02353
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
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: 1.843→1.89 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.328 52 -
Rwork0.314 1205 -
obs--75.45 %

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