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- PDB-3ir4: 1.2 Angstrom Crystal Structure of the Glutaredoxin 2 (grxB) from ... -

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Basic information

Entry
Database: PDB / ID: 3ir4
Title1.2 Angstrom Crystal Structure of the Glutaredoxin 2 (grxB) from Salmonella typhimurium in complex with Glutathione
ComponentsGlutaredoxin 2
KeywordsOXIDOREDUCTASE / Glutaredoxin 2 / Glutathione / idp00895 / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID
Function / homology
Function and homology information


: / cell redox homeostasis / electron transfer activity / cytosol
Similarity search - Function
Glutaredoxin-2 / Glutaredoxin 2, C-terminal / Glutaredoxin 2, C terminal domain / Glutaredoxin active site / Glutaredoxin active site. / Glutathione S-transferase, N-terminal domain / Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 - #10 / Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 / Soluble glutathione S-transferase N-terminal domain profile. / Glutathione S-transferase, N-terminal ...Glutaredoxin-2 / Glutaredoxin 2, C-terminal / Glutaredoxin 2, C terminal domain / Glutaredoxin active site / Glutaredoxin active site. / Glutathione S-transferase, N-terminal domain / Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 - #10 / Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 / Soluble glutathione S-transferase N-terminal domain profile. / Glutathione S-transferase, N-terminal / Glutathione S-transferase, C-terminal domain superfamily / Glutaredoxin / Glutaredoxin / Thioredoxin-like superfamily / Up-down Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
GLUTATHIONE / Glutaredoxin 2
Similarity search - Component
Biological speciesSalmonella enterica subsp. enterica serovar Typhimurium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.2 Å
AuthorsMinasov, G. / Wawrzak, Z. / Skarina, T. / Onopriyenko, O. / Peterson, S.N. / Halavaty, A. / Dauter, Z. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: TO BE PUBLISHED
Title: 1.2 Angstrom Crystal Structure of the Glutaredoxin 2 (grxB) from Salmonella typhimurium in complex with Glutathione.
Authors: Minasov, G. / Wawrzak, Z. / Skarina, T. / Onopriyenko, O. / Peterson, S.N. / Halavaty, A. / Dauter, Z. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
History
DepositionAug 21, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 1, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.2Dec 21, 2011Group: Non-polymer description
Revision 1.3Nov 1, 2017Group: Refinement description / Category: software / Item: _software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Glutaredoxin 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,7286
Polymers25,0971
Non-polymers6315
Water8,809489
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)41.240, 58.760, 87.930
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 2


Mass: 25096.873 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella enterica subsp. enterica serovar Typhimurium (bacteria)
Strain: LT2 / Gene: grxB, STM1165 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-DE3 / References: UniProt: Q7CQR3
#2: Chemical ChemComp-GSH / GLUTATHIONE


Mass: 307.323 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17N3O6S
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 489 / 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: 2.12 Å3/Da / Density % sol: 42.05 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: Protein solution: 0.3M Sodium chloride, 10mM HEPES (pH 7.5); Screen solution: 0.1M Sodium citrate (pH 5.6), 2M Ammonium sulphate, 0.2M Sodium-Potassium tartrate, 5mM Glutathione, 4% (w/v) ...Details: Protein solution: 0.3M Sodium chloride, 10mM HEPES (pH 7.5); Screen solution: 0.1M Sodium citrate (pH 5.6), 2M Ammonium sulphate, 0.2M Sodium-Potassium tartrate, 5mM Glutathione, 4% (w/v) Sucrose; Cryo solution: paratone, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1.0781 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Aug 16, 2009 / Details: Mirrors
RadiationMonochromator: Si {1,1,1} / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0781 Å / Relative weight: 1
ReflectionResolution: 1.2→30 Å / Num. all: 66655 / Num. obs: 66655 / % possible obs: 98.7 % / Observed criterion σ(I): -3 / Redundancy: 5.73 % / Biso Wilson estimate: 6.7 Å2 / Rmerge(I) obs: 0.079 / Net I/σ(I): 14.93
Reflection shellResolution: 1.2→1.22 Å / Redundancy: 5.46 % / Rmerge(I) obs: 0.496 / Mean I/σ(I) obs: 4.04 / Num. unique all: 3133 / % possible all: 96.7

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Processing

Software
NameVersionClassification
Blu-IceMaxdata collection
CRANKphasing
REFMAC5.5.0102refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: SAD / Resolution: 1.2→27.87 Å / Cor.coef. Fo:Fc: 0.978 / Cor.coef. Fo:Fc free: 0.971 / SU B: 0.974 / SU ML: 0.02 / Isotropic thermal model: Mixed (isotropic/anisotropic) / Cross valid method: THROUGHOUT / ESU R: 0.035 / ESU R Free: 0.035 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.14426 3315 5 %RANDOM
Rwork0.11671 ---
all0.11808 63340 --
obs0.11808 63340 98.65 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 6.29 Å2
Baniso -1Baniso -2Baniso -3
1--0.28 Å20 Å20 Å2
2--0.15 Å2-0 Å2
3---0.14 Å2
Refinement stepCycle: LAST / Resolution: 1.2→27.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1740 0 36 489 2265
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0222040
X-RAY DIFFRACTIONr_bond_other_d0.0010.021422
X-RAY DIFFRACTIONr_angle_refined_deg1.5021.9872781
X-RAY DIFFRACTIONr_angle_other_deg0.9583.0013478
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.8015259
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.36723.78995
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.53115375
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.4541517
X-RAY DIFFRACTIONr_chiral_restr0.10.2298
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0212321
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02414
X-RAY DIFFRACTIONr_mcbond_it1.4491.51228
X-RAY DIFFRACTIONr_mcbond_other1.3961.5480
X-RAY DIFFRACTIONr_mcangle_it2.03222010
X-RAY DIFFRACTIONr_scbond_it3.2813812
X-RAY DIFFRACTIONr_scangle_it4.6894.5770
X-RAY DIFFRACTIONr_rigid_bond_restr1.6232040
LS refinement shellResolution: 1.2→1.231 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.179 254 -
Rwork0.146 4519 -
obs-4519 96.91 %
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)
10.0204-0.00570.00380.00840.00570.0082-0.0006-0.0020.00070.00110.0003-0.00030.0003-0.00070.00020.0058-0.0004-0.00010.0014-0.00040.0012-12.5883-9.395828.985
20.0109-0.0001-0.00160.0004-0.00030.00140.00010.00010.00040.0001-0.0001-0.0001-0-0-0.00010.006-0.0003-0.00010.0008-0.00030.0013-14.6673-4.265616.2109
30.0093-0.0057-0.00230.00490.00240.00350.00050.0006-0.0002-0.0003-0.00060.00010.000200.00010.0059-0.00020.00010.00210.00030.0009-17.7262-7.55347.0271
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-2 - 60
2X-RAY DIFFRACTION2A61 - 123
3X-RAY DIFFRACTION3A124 - 215

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