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- PDB-1xw4: Crystal Structure of Human Sulfiredoxin (Srx) in Complex with ADP -

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Basic information

Entry
Database: PDB / ID: 1xw4
TitleCrystal Structure of Human Sulfiredoxin (Srx) in Complex with ADP
ComponentsSulfiredoxin
KeywordsOXIDOREDUCTASE / sulfiredoxin / cysteine / sulfinic acid / peroxiredoxin / sulphiredoxin
Function / homology
Function and homology information


sulfiredoxin / oxidoreductase activity, acting on a sulfur group of donors / sulfiredoxin activity / NFE2L2 regulating anti-oxidant/detoxification enzymes / cellular response to oxidative stress / response to oxidative stress / endoplasmic reticulum membrane / ATP binding / cytosol / cytoplasm
Similarity search - Function
Sulfiredoxin / Conserved hypothetical protein from pyrococcus furiosus pfu- 392566-001, ParB domain / Conserved hypothetical protein from pyrococcus furiosus pfu- 392566-001, ParB domain / ParB/Sulfiredoxin domain / ParB/Sulfiredoxin / ParB-like nuclease domain / ParB/Sulfiredoxin superfamily / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / Sulfiredoxin-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsMurray, M.S. / Jonsson, T.J. / Johnson, L.C. / Poole, L.B. / Lowther, W.T.
CitationJournal: Biochemistry / Year: 2005
Title: Structural basis for the retroreduction of inactivated peroxiredoxins by human sulfiredoxin.
Authors: Jonsson, T.J. / Murray, M.S. / Johnson, L.C. / Poole, L.B. / Lowther, W.T.
History
DepositionOct 29, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 24, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 24, 2019Group: Data collection / Derived calculations / Refinement description
Category: software / struct_conn
Item: _software.classification / _software.name ..._software.classification / _software.name / _software.version / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4Aug 23, 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

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Assembly

Deposited unit
X: Sulfiredoxin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,4942
Polymers12,0671
Non-polymers4271
Water1,27971
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)68.451, 68.451, 50.891
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 Sulfiredoxin /


Mass: 12066.685 Da / Num. of mol.: 1 / Mutation: residues 32-137
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pet19 / Production host: Escherichia coli (E. coli) / Strain (production host): C41(DE3) / References: UniProt: Q9BYN0
#2: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / Adenosine diphosphate


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 71 / 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: 2.9 Å3/Da / Density % sol: 56.7 %
Crystal growTemperature: 293 K / pH: 7.5
Details: MPD, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K, pH 7.50

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418
DetectorType: RIGAKU / Detector: IMAGE PLATE / Date: Jul 9, 2004 / Details: CONFOCAL BLUE MAX-FLUX
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→29.64 Å / Num. obs: 9562 / % possible obs: 99.6 % / Observed criterion σ(I): 0 / Redundancy: 9.63 % / Rmerge(I) obs: 0.051 / Net I/σ(I): 30.9
Reflection shellResolution: 2→2.07 Å / Redundancy: 5.03 % / Mean I/σ(I) obs: 4.4 / % possible all: 95.3

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
d*TREKdata reduction
CNSrefinement
CNSphasing
d*TREKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1XW3

1xw3


Resolution: 2→29.6 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.917 / SU B: 4.501 / SU ML: 0.128 / Cross valid method: THROUGHOUT / ESU R: 0.187 / ESU R Free: 0.177 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27084 456 4.8 %RANDOM
Rwork0.21825 ---
obs0.22068 9084 99.43 %-
all-9602 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 27.872 Å2
Baniso -1Baniso -2Baniso -3
1-0.54 Å20.27 Å20 Å2
2--0.54 Å20 Å2
3----0.81 Å2
Refine analyzeLuzzati coordinate error obs: 0.36 Å / Luzzati sigma a obs: 0.23 Å
Refinement stepCycle: LAST / Resolution: 2→29.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms840 0 27 71 938
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.022890
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.8282.0241222
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4795107
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.15823.33336
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.4215134
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.855156
X-RAY DIFFRACTIONr_chiral_restr0.1150.2139
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02669
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2160.2326
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3010.2593
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2240.267
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.240.240
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1080.210
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.1261.5553
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.8342882
X-RAY DIFFRACTIONr_scbond_it2.7783384
X-RAY DIFFRACTIONr_scangle_it4.3574.5340
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.001→2.053 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.332 37 -
Rwork0.278 613 -
obs--93.93 %

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