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- PDB-3fz9: Crystal structure of poplar glutaredoxin S12 in complex with glut... -

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Basic information

Entry
Database: PDB / ID: 3fz9
TitleCrystal structure of poplar glutaredoxin S12 in complex with glutathione
ComponentsGlutaredoxin
KeywordsOXIDOREDUCTASE / Glutaredoxin
Function / homologyGlutaredoxin / Glutaredoxin / 3-Layer(aba) Sandwich / Alpha Beta / GLUTATHIONE
Function and homology information
Biological speciesPopulus tremula x Populus tremuloides (plant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsDidierjean, C. / Corbier, C. / Koh, C.S. / Rouhier, N. / Jacquot, J.P.
CitationJournal: J.Biol.Chem. / Year: 2009
Title: Structure-function relationship of the chloroplastic glutaredoxin S12 with an atypical WCSYS active site.
Authors: Couturier, J. / Koh, C.S. / Zaffagnini, M. / Winger, A.M. / Gualberto, J.M. / Corbier, C. / Decottignies, P. / Jacquot, J.P. / Lemaire, S.D. / Didierjean, C. / Rouhier, N.
History
DepositionJan 24, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 24, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 6, 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 / diffrn_source / 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 / _diffrn_source.pdbx_synchrotron_site / _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

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Assembly

Deposited unit
A: Glutaredoxin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,5532
Polymers12,2461
Non-polymers3071
Water3,351186
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)39.032, 47.265, 55.620
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


Mass: 12245.981 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Populus tremula x Populus tremuloides (plant)
Gene: GrxS12 / Organ: leaf / Plasmid: pSBET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
#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.: 186 / 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: 2.09 Å3/Da / Density % sol: 41.29 %
Crystal growTemperature: 293.15 K / Method: microbatch under oil / pH: 7.5
Details: 0.1 M Na HEPES (pH 7.5) and 20 % PEG 8000, microbatch under oil, temperature 293.15K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.815 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Aug 22, 2007
RadiationMonochromator: Ge(111) triangular bent, compressing 7 deg. Fankuchen cut
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.815 Å / Relative weight: 1
ReflectionResolution: 1.7→50 Å / Num. obs: 11857 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.5 % / Rmerge(I) obs: 0.045 / Net I/σ(I): 13.4
Reflection shellResolution: 1.7→1.73 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.24 / Mean I/σ(I) obs: 2.3 / % possible all: 95

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Processing

Software
NameVersionClassification
HKL-2000data collection
MOLREPphasing
REFMAC5.2.0019refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2FLS

2fls


Resolution: 1.7→31.94 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.923 / SU B: 2.446 / SU ML: 0.083 / Cross valid method: THROUGHOUT / ESU R: 0.126 / ESU R Free: 0.124 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23761 564 4.8 %RANDOM
Rwork0.19201 ---
obs0.19424 11233 99.26 %-
all-11234 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 20.446 Å2
Baniso -1Baniso -2Baniso -3
1--0.02 Å20 Å20 Å2
2--0.03 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.7→31.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms819 0 20 186 1025
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.022851
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3972.0091148
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.525105
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.79425.15233
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.21715156
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.609154
X-RAY DIFFRACTIONr_chiral_restr0.0850.2133
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02620
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2180.2421
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3030.2580
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1420.2130
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1620.227
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1470.214
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.8571.5539
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.3792850
X-RAY DIFFRACTIONr_scbond_it2.4793347
X-RAY DIFFRACTIONr_scangle_it3.8444.5298
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.696→1.74 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.25 27 -
Rwork0.238 744 -
obs--91.9 %

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