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- PDB-1qmv: thioredoxin peroxidase B from red blood cells -

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Basic information

Entry
Database: PDB / ID: 1qmv
Titlethioredoxin peroxidase B from red blood cells
ComponentsPEROXIREDOXIN-2
KeywordsOXIDOREDUCTASE / SULPHINIC ACID / THIOREDOXIN
Function / homology
Function and homology information


respiratory burst involved in inflammatory response / negative regulation of T cell differentiation / leukocyte activation / regulation of hydrogen peroxide metabolic process / thioredoxin-dependent peroxiredoxin / negative regulation of lipopolysaccharide-mediated signaling pathway / thioredoxin peroxidase activity / defense response to tumor cell / Deregulated CDK5 triggers multiple neurodegenerative pathways in Alzheimer's disease models / Detoxification of Reactive Oxygen Species ...respiratory burst involved in inflammatory response / negative regulation of T cell differentiation / leukocyte activation / regulation of hydrogen peroxide metabolic process / thioredoxin-dependent peroxiredoxin / negative regulation of lipopolysaccharide-mediated signaling pathway / thioredoxin peroxidase activity / defense response to tumor cell / Deregulated CDK5 triggers multiple neurodegenerative pathways in Alzheimer's disease models / Detoxification of Reactive Oxygen Species / antioxidant activity / T cell homeostasis / positive regulation of blood coagulation / negative regulation of extrinsic apoptotic signaling pathway in absence of ligand / T cell proliferation / extrinsic apoptotic signaling pathway / removal of superoxide radicals / cell redox homeostasis / thymus development / hydrogen peroxide catabolic process / TP53 Regulates Metabolic Genes / response to oxidative stress / cellular response to oxidative stress / regulation of apoptotic process / response to lipopolysaccharide / positive regulation of MAPK cascade / negative regulation of apoptotic process / extracellular exosome / cytoplasm / cytosol
Similarity search - Function
Peroxiredoxin, AhpC-type / : / Peroxiredoxin, C-terminal / C-terminal domain of 1-Cys peroxiredoxin / Alkyl hydroperoxide reductase subunit C/ Thiol specific antioxidant / AhpC/TSA family / Thioredoxin domain profile. / Thioredoxin domain / Glutaredoxin / Glutaredoxin ...Peroxiredoxin, AhpC-type / : / Peroxiredoxin, C-terminal / C-terminal domain of 1-Cys peroxiredoxin / Alkyl hydroperoxide reductase subunit C/ Thiol specific antioxidant / AhpC/TSA family / 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: 1.7 Å
AuthorsIsupov, M.N. / Littlechild, J.A. / Lebedev, A.A. / Errington, N. / Vagin, A.A. / Schroder, E.
Citation
Journal: Structure / Year: 2000
Title: Crystal Structure of Decameric 2-Cys Peroxiredoxin from Human Erythrocytes at 1.7 A Resolution.
Authors: Schroder, E. / Littlechild, J.A. / Lebedev, A.A. / Errington, N. / Vagin, A.A. / Isupov, M.N.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 1999
Title: Crystallisation and Preliminary X-Ray Analysis of Human Thioredoxin Peroxidase B from Red Blood Cells
Authors: Schroder, E. / Isupov, M.N. / Naran, A. / Littlechild, J.A.
#2: Journal: Protein Sci. / Year: 1998
Title: Evidence that Peroxiredoxins are Novel Members of the Thioredoxin Fold Superfamily
Authors: Schroder, E. / Ponting, C.P.
#3: Journal: Biochim.Biophys.Acta / Year: 1998
Title: Porcine Natural Killer Enhancing Factor-B: Oligomerization and Identification as a Calpain Substrate in-Vitro
Authors: Schroder, E. / Willis, A.C. / Ponting, C.P.
History
DepositionOct 7, 1999Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 28, 2000Provider: repository / Type: Initial release
Revision 1.1Jan 30, 2013Group: Advisory / Database references ...Advisory / Database references / Derived calculations / Non-polymer description / Other / Structure summary / Version format compliance
Revision 1.2Oct 22, 2014Group: Database references / Other
Revision 1.3Jul 24, 2019Group: Data collection / Derived calculations / Category: diffrn_source / struct_conn
Item: _diffrn_source.pdbx_synchrotron_site / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf
Revision 1.5Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PEROXIREDOXIN-2
B: PEROXIREDOXIN-2
C: PEROXIREDOXIN-2
D: PEROXIREDOXIN-2
E: PEROXIREDOXIN-2
F: PEROXIREDOXIN-2
G: PEROXIREDOXIN-2
H: PEROXIREDOXIN-2
I: PEROXIREDOXIN-2
J: PEROXIREDOXIN-2


Theoretical massNumber of molelcules
Total (without water)218,62710
Polymers218,62710
Non-polymers00
Water39,5252194
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area28180 Å2
ΔGint-184.5 kcal/mol
Surface area70240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.880, 107.030, 119.500
Angle α, β, γ (deg.)90.00, 110.87, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.02487, -0.49699, 0.8674), (-0.48537, -0.75254, -0.44509), (0.87396, -0.43208, -0.2225)-47.28796, 23.68375, 66.40012
2given(0.45736, 0.24239, -0.85561), (0.33504, 0.84427, 0.41827), (0.82375, -0.47797, 0.30493)48.09451, -22.24361, 36.8665
3given(-0.88075, -0.0263, 0.47285), (-0.05844, -0.98479, -0.16361), (0.46997, -0.17173, 0.86582)-23.84083, 8.51847, 6.61718
4given(0.49232, 0.36289, 0.79116), (0.24977, 0.81182, -0.52779), (-0.83381, 0.45745, 0.30904)-42.63705, 29.35084, 38.57346
5given(0.49895, -0.8601, 0.1062), (-0.86306, -0.50426, -0.02912), (0.0786, -0.07713, -0.99392)-6.14907, 1.89981, 108.705
6given(-0.3892, 0.73123, -0.5602), (0.78609, 0.58068, 0.21182), (0.48019, -0.35793, -0.80082)32.80054, -10.84413, 97.23035
7given(-0.83117, -0.10913, -0.5452), (-0.12928, -0.91574, 0.38039), (-0.54077, 0.38665, 0.74704)31.90295, -20.12766, 13.62314
8given(-0.33979, 0.81446, 0.47031), (0.76427, 0.53055, -0.3666), (-0.54812, 0.23488, -0.80275)-24.78926, 19.57494, 98.82507
9given(0.02141, -0.65561, -0.7548), (-0.60353, -0.61037, 0.51303), (-0.79705, 0.44456, -0.40874)41.22491, -28.4704, 77.49481

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Components

#1: Protein
PEROXIREDOXIN-2 / NATURAL KILLER CELL-ENHANCING FACTOR B / NKEF-B / PRP / THIOL-SPECIFIC ANTIOXIDANT PROTEIN / TSA / ...NATURAL KILLER CELL-ENHANCING FACTOR B / NKEF-B / PRP / THIOL-SPECIFIC ANTIOXIDANT PROTEIN / TSA / THIOREDOXIN PEROXIDASE 1 / THIOREDOXIN PEROXIDASE-B / THIOREDOXIN-DEPENDENT PEROXIDE REDUCTASE 1 / 2-CYS PEROXIREDOXIN / CALPROMOTIN


Mass: 21862.715 Da / Num. of mol.: 10 / Source method: isolated from a natural source / Details: PURIFIED FROM ONE MONTH OLD BLOOD / Source: (natural) HOMO SAPIENS (human) / Cell: ERYTHROCYTE / Cellular location: CYTOPLASM / Organ: BLOOD / References: UniProt: P32119, peroxiredoxin
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2194 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.4 Å3/Da / Density % sol: 49 %
Crystal growpH: 7.5
Details: 16 % (V/V) PEG 400, 100 MM TRIS-HCL, PH 7.5, 10 % (V/V) 2-PROPANOL, 10 MM DITHIOERYTHREITOL
Crystal grow
*PLUS
Temperature: 290 K / Method: vapor diffusion, hanging drop
Details: drop consists of equal volume of protein and reservoir solutions
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
115 mg/mlprotein1drop
225 mMTris-HCl1drop
35 mMEDTA1drop
410 mMdithiothreitol1drop
516 %(v/v)PEG4001reservoir
6100 mMTris-HCl1reservoir
710 %(v/v)2-propanol1reservoir
810 mMdithiothreitol1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.9076
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jul 15, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9076 Å / Relative weight: 1
ReflectionResolution: 1.7→20 Å / Num. obs: 228010 / % possible obs: 99.6 % / Redundancy: 4.2 % / Biso Wilson estimate: 34.1 Å2 / Rsym value: 0.057 / Net I/σ(I): 18.8
Reflection shellResolution: 1.7→1.73 Å / Redundancy: 3 % / Mean I/σ(I) obs: 1.7 / Rsym value: 0.493 / % possible all: 93.6
Reflection
*PLUS
Rmerge(I) obs: 0.057
Reflection shell
*PLUS
% possible obs: 93.6 % / Redundancy: 2.3 % / Rmerge(I) obs: 0.481 / Mean I/σ(I) obs: 2.07

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
MOLREPphasing
REFMACrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1PRX

1prx


Resolution: 1.7→20 Å / SU B: 2.67 / SU ML: 0.084 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.1106 / ESU R Free: 0.122
RfactorNum. reflection% reflectionSelection details
Rfree0.256 2287 1 %RANDOM
Rwork0.192 ---
obs-225682 98.6 %-
Displacement parametersBiso mean: 32.7 Å2
Baniso -1Baniso -2Baniso -3
1--7.341 Å20 Å2-1.201 Å2
2--18.791 Å20 Å2
3----11.027 Å2
Refinement stepCycle: LAST / Resolution: 1.7→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15440 0 0 2194 17634
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0110.02
X-RAY DIFFRACTIONp_angle_d0.0270.04
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0310.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it2.4674
X-RAY DIFFRACTIONp_mcangle_it3.0716
X-RAY DIFFRACTIONp_scbond_it4.6758
X-RAY DIFFRACTIONp_scangle_it5.84910
X-RAY DIFFRACTIONp_plane_restr0.0220.03
X-RAY DIFFRACTIONp_chiral_restr0.1460.15
X-RAY DIFFRACTIONp_singtor_nbd0.1730.3
X-RAY DIFFRACTIONp_multtor_nbd0.2460.3
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd0.1220.3
X-RAY DIFFRACTIONp_planar_tor4.27
X-RAY DIFFRACTIONp_staggered_tor14.315
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor26.920
X-RAY DIFFRACTIONp_special_tor

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