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- PDB-3uiw: Zebrafish Grx2 (APO) -

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Basic information

Entry
Database: PDB / ID: 3uiw
TitleZebrafish Grx2 (APO)
ComponentsGlutaredoxin 2
KeywordsOXIDOREDUCTASE / Thioredoxin/glutaredoxin fold / glutathione / 2Fe2S cluster
Function / homology
Function and homology information


neural crest cell migration involved in heart formation / heart formation / glutathione disulfide oxidoreductase activity / glial cell migration / vasculature development / neural crest cell migration / central nervous system development / 2 iron, 2 sulfur cluster binding / cellular response to oxidative stress / oxidoreductase activity ...neural crest cell migration involved in heart formation / heart formation / glutathione disulfide oxidoreductase activity / glial cell migration / vasculature development / neural crest cell migration / central nervous system development / 2 iron, 2 sulfur cluster binding / cellular response to oxidative stress / oxidoreductase activity / mitochondrion / cytoplasm / cytosol
Similarity search - Function
Glutaredoxin subgroup / Glutaredoxin, eukaryotic/virial / Glutaredoxin active site / Glutaredoxin active site. / Glutaredoxin / Glutaredoxin / Glutaredoxin domain profile. / Glutaredoxin / Glutaredoxin / Thioredoxin-like superfamily ...Glutaredoxin subgroup / Glutaredoxin, eukaryotic/virial / Glutaredoxin active site / Glutaredoxin active site. / 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 speciesDanio rerio (zebrafish)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.601 Å
AuthorsMcDonough, M.A. / Johansson, C.
CitationJournal: To be Published
Title: A New Mode of Iron-sulfur Cluster Coordination in Glutaredoxins is Crucial for Axonogenesis
Authors: Brautigam, L. / Johansson, C. / Kubsch, B. / McDonough, M.A. / Bill, E. / Holmgren, A. / Berndt, C.
History
DepositionNov 6, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 27, 2013Provider: repository / Type: Initial release
Revision 1.1Sep 13, 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
B: Glutaredoxin 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,8985
Polymers33,1872
Non-polymers7113
Water84747
1
A: Glutaredoxin 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,9973
Polymers16,5941
Non-polymers4032
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Glutaredoxin 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,9012
Polymers16,5941
Non-polymers3071
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
A: Glutaredoxin 2
B: Glutaredoxin 2
hetero molecules

A: Glutaredoxin 2
B: Glutaredoxin 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,79610
Polymers66,3754
Non-polymers1,4216
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555-x,-x+y,-z1
Buried area7000 Å2
ΔGint-103 kcal/mol
Surface area20600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.552, 92.552, 167.077
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11A-305-

HOH

21A-307-

HOH

31A-319-

HOH

41A-320-

HOH

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Components

#1: Protein Glutaredoxin 2


Mass: 16593.668 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Danio rerio (zebrafish) / Gene: Dr.88731, glrx2, zgc:92698 / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q6DH06
#2: Chemical ChemComp-GSH / GLUTATHIONE


Mass: 307.323 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H17N3O6S
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 47 / 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: 2.07 Å3/Da / Density % sol: 40.72 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5
Details: 0.3 M potassium sodium tartrate, 2 M ammonium sulfate, 0.1 m citrate, pH 5.0, VAPOR DIFFUSION, SITTING DROP, temperature 298.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: Mar 12, 2011 / Details: Varimax HF
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionRedundancy: 5.4 % / Av σ(I) over netI: 17.27 / Number: 47409 / Rmerge(I) obs: 0.073 / Χ2: 1.03 / D res high: 2.6 Å / D res low: 40 Å / Num. obs: 8711 / % possible obs: 99.7
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
5.6409810.0380.9815
4.445.699.810.0441.0295.4
3.884.4499.910.051.0875.4
3.533.8810010.0641.0065.5
3.283.5310010.0851.0275.6
3.083.2810010.1151.0415.6
2.933.0810010.1821.0585.5
2.82.9310010.2441.0185.5
2.692.810010.3990.9795.5
2.62.6910010.5551.1155.5
ReflectionResolution: 2.6→40 Å / Num. obs: 8711 / % possible obs: 99.7 % / Observed criterion σ(I): 1 / Redundancy: 5.4 % / Biso Wilson estimate: 37 Å2 / Rmerge(I) obs: 0.073 / Χ2: 1.034 / Net I/σ(I): 14
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.6-2.695.50.5558601.1151100
2.69-2.85.50.3998620.9791100
2.8-2.935.50.2448521.0181100
2.93-3.085.50.1828771.0581100
3.08-3.285.60.1158461.0411100
3.28-3.535.60.0858711.0271100
3.53-3.885.50.0648741.0061100
3.88-4.445.40.058681.087199.9
4.44-5.65.40.0448811.029199.8
5.6-4050.0389200.981198

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation2.8 Å24.52 Å
Translation2.8 Å24.52 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
PHENIX1.7_650refinement
PDB_EXTRACT3.1data extraction
CrystalCleardata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2FLS

2fls


Resolution: 2.601→25.665 Å / Occupancy max: 1 / Occupancy min: 0.75 / SU ML: 0.37 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 24.56 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2502 770 9.94 %10%
Rwork0.1891 ---
obs0.1952 7744 88.79 %-
Solvent computationShrinkage radii: 0.89 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 40 Å2 / ksol: 0.429 e/Å3
Displacement parametersBiso max: 159.41 Å2 / Biso mean: 48.7466 Å2 / Biso min: 4.58 Å2
Baniso -1Baniso -2Baniso -3
1-8.6633 Å20 Å2-0 Å2
2--8.6633 Å20 Å2
3----6.8092 Å2
Refinement stepCycle: LAST / Resolution: 2.601→25.665 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1589 0 45 47 1681
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0141660
X-RAY DIFFRACTIONf_angle_d1.2422241
X-RAY DIFFRACTIONf_chiral_restr0.064264
X-RAY DIFFRACTIONf_plane_restr0.005292
X-RAY DIFFRACTIONf_dihedral_angle_d17.403612
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 6

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.6012-2.76390.3491010.298488098168
2.7639-2.97710.31861190.21611042116181
2.9771-3.27610.24231260.1721168129491
3.2761-3.74890.23241340.16821266140097
3.7489-4.71840.19961400.14621278141897
4.7184-25.66580.27131500.22471340149098
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)
10.0125-0.02090.01110.0418-0.0320.03050.0466-0.1075-0.05790.01310.07360.07690.1516-0.13440.2084-0.07070.1425-0.23620.04780.3293-0.3962-35.600618.6438-1.1782
20.1412-0.03260.01310.2996-0.25840.79880.11860.0529-0.18350.0613-0.04610.02690.0790.34650.05960.0430.0228-0.03230.0773-0.00920.1109-30.538122.9381-14.8347
30.15170.1069-0.09190.0985-0.09650.2854-0.00710.05640.28620.01870.18120.1782-0.1839-0.03920.0650.1733-0.001-0.02580.0835-0.01370.189-28.750637.1122-13.6524
40.0061-0.00640.00510.0021-0.00070.0090.0121-0.05580.08540.05370.14790.14110.0701-0.00690.00010.18210.0482-0.03240.3563-0.10770.4047-20.860531.87543.0634
50.0027-0.00170.0107-0.0008-0.00350.0075-0.0564-0.0599-0.03690.04480.16490.01670.1124-0.0923-0.00020.4862-0.0608-0.05590.20910.08060.2713-31.620811.45490.739
60.09980.07690.05430.03950.0550.06250.05080.1364-0.07930.34290.1946-0.2287-0.0993-0.14890.00690.54330.025-0.14560.37380.10450.2924-21.379616.220916.7626
70.0025-0.0005-0.00480.00760.0060.01210.0622-0.03950.00280.0223-0.04170.1036-0.0488-0.170.00010.5060.104-0.19430.3351-0.00350.3773-21.947220.140411.9249
80.0246-0.01720.01820.0033-0.00150.00440.0036-0.13090.170.19110.02440.05850.1044-0.34580.00010.5557-0.00120.01540.439-0.0030.3431-34.492711.310912.2081
90.0365-0.01320.01860.0057-0.00620.00590.08870.0720.0262-0.04520.04250.01420.05780.00450.17940.3640.0177-0.23170.33540.38060.5026-24.14278.340312.8013
100.04560.0021-0.05180.03520.01190.07-0.1-0.0885-0.03740.0832-0.0111-0.10410.03890.0686-0.07730.73320.1421-0.47750.32670.23660.57-15.63167.610116.75
110.0046-0.01460.01490.053-0.06630.08510.0611-0.0226-0.0165-0.0140.0812-0.01530.0159-0.01520.07560.37350.52120.04550.30470.21510.6808-8.79410.317610.516
120.00110.00140.0012-0-0.00060.00070.1278-0.0159-0.00870.0206-0.0126-0.0660.0097-0.0462-0.00010.55460.1454-0.12280.4509-0.08640.5373-11.874217.3173-2.609
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resseq 9:25)A9 - 25
2X-RAY DIFFRACTION2chain 'A' and (resseq 26:88)A26 - 88
3X-RAY DIFFRACTION3chain 'A' and (resseq 89:112)A89 - 112
4X-RAY DIFFRACTION4chain 'A' and (resseq 113:118)A113 - 118
5X-RAY DIFFRACTION5chain 'B' and (resseq 10:25)B10 - 25
6X-RAY DIFFRACTION6chain 'B' and (resseq 26:50)B26 - 50
7X-RAY DIFFRACTION7chain 'B' and (resseq 51:58)B51 - 58
8X-RAY DIFFRACTION8chain 'B' and (resseq 59:76)B59 - 76
9X-RAY DIFFRACTION9chain 'B' and (resseq 77:88)B77 - 88
10X-RAY DIFFRACTION10chain 'B' and (resseq 89:102)B89 - 102
11X-RAY DIFFRACTION11chain 'B' and (resseq 103:111)B103 - 111
12X-RAY DIFFRACTION12chain 'B' and (resseq 112:118)B112 - 118

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