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- PDB-4h86: Crystal structure of Ahp1 from Saccharomyces cerevisiae in reduce... -

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Basic information

Entry
Database: PDB / ID: 4h86
TitleCrystal structure of Ahp1 from Saccharomyces cerevisiae in reduced form
ComponentsPeroxiredoxin type-2
KeywordsOXIDOREDUCTASE / Peroxiredoxin type-2
Function / homology
Function and homology information


TP53 Regulates Metabolic Genes / Detoxification of Reactive Oxygen Species / thioredoxin-dependent peroxiredoxin / thioredoxin peroxidase activity / response to metal ion / cell redox homeostasis / hydrogen peroxide catabolic process / peroxisome / cellular response to oxidative stress / mitochondrion ...TP53 Regulates Metabolic Genes / Detoxification of Reactive Oxygen Species / thioredoxin-dependent peroxiredoxin / thioredoxin peroxidase activity / response to metal ion / cell redox homeostasis / hydrogen peroxide catabolic process / peroxisome / cellular response to oxidative stress / mitochondrion / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Peroxiredoxin-5-like / Redoxin / Redoxin / Thioredoxin domain profile. / Thioredoxin domain / Glutaredoxin / Glutaredoxin / Thioredoxin-like superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.004 Å
AuthorsLiu, M. / Wang, F. / Qiu, R. / Wu, T. / Gu, S. / Tang, R. / Ji, C.
CitationJournal: To be Published
Title: Crystal structure of Ahp1 from Saccharomyces cerevisiae in reduced form
Authors: Liu, M. / Wang, F. / Qiu, R. / Wu, T. / Gu, S. / Tang, R. / Ji, C.
History
DepositionSep 21, 2012Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 10, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.2Nov 8, 2023Group: Data collection / Database references / 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Peroxiredoxin type-2


Theoretical massNumber of molelcules
Total (without water)21,5931
Polymers21,5931
Non-polymers00
Water4,432246
1
A: Peroxiredoxin type-2

A: Peroxiredoxin type-2


Theoretical massNumber of molelcules
Total (without water)43,1872
Polymers43,1872
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation16_566x,-y+1,-z+3/21
Buried area1130 Å2
ΔGint-13 kcal/mol
Surface area17230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)149.049, 149.049, 149.049
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number199
Space group name H-MI213
Components on special symmetry positions
IDModelComponents
11A-236-

HOH

21A-433-

HOH

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Components

#1: Protein Peroxiredoxin type-2 / AHPC1 / Cytoplasmic thiol peroxidase 3 / cTPx 3 / Peroxiredoxin type II / Peroxisomal alkyl ...AHPC1 / Cytoplasmic thiol peroxidase 3 / cTPx 3 / Peroxiredoxin type II / Peroxisomal alkyl hydroperoxide reductase / TPx type II / Thiol-specific antioxidant II / TSA II / Thioredoxin peroxidase type II / Thioredoxin reductase type II


Mass: 21593.324 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: ATCC 204508 / S288c / Gene: AHP1, YLR109W, L2916, L9354.5 / Production host: Escherichia coli (E. coli) / References: UniProt: P38013, peroxiredoxin
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 246 / 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: 6.39 Å3/Da / Density % sol: 80.75 % / Mosaicity: 0.251 °
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.4
Details: Protein Solution (40 mg/ml Ahp1 protein, in Milli-Q water containing 10mM DTT) mixed in a 1:1 ratio with the well solution (0.1 M BIS-TRIS pH 5.4, 2.0 M Ammonium Sulfate) Cryoprotected with ...Details: Protein Solution (40 mg/ml Ahp1 protein, in Milli-Q water containing 10mM DTT) mixed in a 1:1 ratio with the well solution (0.1 M BIS-TRIS pH 5.4, 2.0 M Ammonium Sulfate) Cryoprotected with 20% Glycerol , VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.97915 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Nov 8, 2011
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. all: 37056 / Num. obs: 37056 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 44.8 % / Biso Wilson estimate: 29.79 Å2 / Rmerge(I) obs: 0.125 / Χ2: 2.82 / Net I/σ(I): 9
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2-2.03450.76518441.2631100
2.03-2.0744.90.65518501.4031100
2.07-2.1145.10.53518201.3181100
2.11-2.1544.90.43718631.361100
2.15-2.2450.38218171.4081100
2.2-2.2545.10.37818481.6081100
2.25-2.31450.32618411.4651100
2.31-2.37450.27218441.5521100
2.37-2.4445.10.25618371.6951100
2.44-2.52450.23618331.9041100
2.52-2.6145.10.22218352.1561100
2.61-2.7144.80.21118522.5361100
2.71-2.84450.18118633.1381100
2.84-2.9944.80.16918333.8691100
2.99-3.1744.70.14718504.3531100
3.17-3.4244.30.11718634.5521100
3.42-3.7643.40.09618604.8361100
3.76-4.3144.70.08418725.2471100
4.31-5.4345.30.07918845.3061100
5.43-5043.40.07619475.349199.7

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHENIX1.8_1069refinement
PDB_EXTRACT3.11data extraction
HKL-2000data collection
HKL-2000data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRIES 1TP9, 3UMA, 1NM3 AND 2PWJ

1tp9

3uma

1nm3

2pwj


Resolution: 2.004→35.131 Å / Occupancy max: 1 / Occupancy min: 0.03 / FOM work R set: 0.889 / SU ML: 0.15 / σ(F): 1.33 / Phase error: 17.55 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1734 1863 5.03 %RANDOM
Rwork0.1576 ---
all0.1584 37055 --
obs0.1584 37007 99.87 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 116.29 Å2 / Biso mean: 33.7781 Å2 / Biso min: 15.74 Å2
Refinement stepCycle: LAST / Resolution: 2.004→35.131 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1422 0 0 246 1668
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061484
X-RAY DIFFRACTIONf_angle_d0.9072024
X-RAY DIFFRACTIONf_chiral_restr0.066230
X-RAY DIFFRACTIONf_plane_restr0.004260
X-RAY DIFFRACTIONf_dihedral_angle_d11.438530
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 13 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.0036-2.05780.20481380.186226902828
2.0578-2.11830.21691450.171926862831
2.1183-2.18670.18591400.16326772817
2.1867-2.26480.20051430.165227072850
2.2648-2.35550.181410.175926762817
2.3555-2.46260.20061450.172726662811
2.4626-2.59240.2421410.172627032844
2.5924-2.75480.20671430.174426852828
2.7548-2.96740.16641400.165526892829
2.9674-3.26580.17221480.159127102858
3.2658-3.73790.14481420.138827212863
3.7379-4.70760.1391470.126127152862
4.7076-35.13660.17951500.171428192969

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