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- PDB-4fh8: Crystal Structure of Peroxiredoxin-1 from the human hookworm Ancy... -

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Basic information

Entry
Database: PDB / ID: 4fh8
TitleCrystal Structure of Peroxiredoxin-1 from the human hookworm Ancylostoma ceylanicum
ComponentsAcePrx-1
KeywordsOXIDOREDUCTASE / 2-cys peroxiredoxin
Function / homology
Function and homology information


thioredoxin-dependent peroxiredoxin / peroxiredoxin activity
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 / Thioredoxin-like superfamily ...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
thioredoxin-dependent peroxiredoxin
Similarity search - Component
Biological speciesAncylostoma ceylanicum (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.11 Å
AuthorsNguyen, J.B. / Modis, Y.
CitationJournal: Chem.Biol. / Year: 2013
Title: Peroxiredoxin-1 from the Human Hookworm Ancylostoma ceylanicum Forms a Stable Oxidized Decamer and Is Covalently Inhibited by Conoidin A.
Authors: Nguyen, J.B. / Pool, C.D. / Wong, C.Y. / Treger, R.S. / Williams, D.L. / Cappello, M. / Lea, W.A. / Simeonov, A. / Vermeire, J.J. / Modis, Y.
History
DepositionJun 5, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 12, 2013Provider: repository / Type: Initial release
Revision 1.1Aug 14, 2013Group: Database references
Revision 1.2Sep 11, 2013Group: Database references
Revision 1.3Sep 13, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: AcePrx-1
B: AcePrx-1
C: AcePrx-1
D: AcePrx-1
E: AcePrx-1
F: AcePrx-1
G: AcePrx-1
H: AcePrx-1
I: AcePrx-1
J: AcePrx-1


Theoretical massNumber of molelcules
Total (without water)229,98310
Polymers229,98310
Non-polymers00
Water10,899605
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area17840 Å2
ΔGint-120 kcal/mol
Surface area70290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.688, 146.282, 136.030
Angle α, β, γ (deg.)90.00, 95.24, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
AcePrx-1 / Peroxiredoxin-1


Mass: 22998.312 Da / Num. of mol.: 10
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ancylostoma ceylanicum (invertebrata) / Plasmid: pET16b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: J7HJM3*PLUS, peroxiredoxin
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 605 / 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: 2.79 Å3/Da / Density % sol: 55.86 %
Crystal growTemperature: 285 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 6-8% PEG3350, 0.1 M MES, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 285K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 29, 2012
RadiationMonochromator: Rosenbaum-Rock double crystal sagittal focusing
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2.11→46.55 Å / Num. all: 144443 / Num. obs: 144094 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4 % / Biso Wilson estimate: 39.28 Å2 / Rmerge(I) obs: 0.063 / Net I/σ(I): 20.63
Reflection shellResolution: 2.11→2.15 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.643 / Mean I/σ(I) obs: 2.03 / % possible all: 95.5

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Processing

Software
NameVersionClassification
CBASSdata collection
PHASERphasing
REFMAC5.6.0117refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1QMV

1qmv


Resolution: 2.11→46.55 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.958 / SU B: 10.618 / SU ML: 0.126 / Cross valid method: THROUGHOUT / σ(F): 1 / ESU R: 0.174 / ESU R Free: 0.147 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT' U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.21364 7228 5 %RANDOM
Rwork0.19459 ---
obs0.19556 136789 99.71 %-
all-144443 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 48.669 Å2
Baniso -1Baniso -2Baniso -3
1-2.21 Å2-0 Å2-4.19 Å2
2---3.37 Å20 Å2
3---0.4 Å2
Refinement stepCycle: LAST / Resolution: 2.11→46.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13404 0 0 605 14009
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0213751
X-RAY DIFFRACTIONr_angle_refined_deg0.9491.95718646
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.24451684
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.75723.981623
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.674152261
X-RAY DIFFRACTIONr_dihedral_angle_4_deg6.5021560
X-RAY DIFFRACTIONr_chiral_restr0.0660.22071
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.02110458
LS refinement shellResolution: 2.11→2.165 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.319 542 -
Rwork0.302 9743 -
obs--97.65 %
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)
11.133-0.74430.29391.8074-0.40290.83270.0016-0.0149-0.0153-0.0099-0.02220.0087-0.08770.00590.02060.0707-0.01770.08930.1862-0.03020.1486.595336.51164.9383
21.6081-0.16361.06771.1252-0.05541.8011-0.08020.16490.1084-0.10640.0295-0.0748-0.18140.21330.05060.1148-0.05390.08960.2353-0.0030.10099.094148.510541.6369
31.5190.53971.15561.58820.66572.1456-0.1683-0.15360.203-0.2194-0.02890.2659-0.3041-0.21330.19720.12870.0667-0.01350.1850.00310.119-19.298446.560823.1823
41.38420.9920.66613.2150.7381.7926-0.20340.06330.0253-0.5010.18190.0873-0.26720.07990.02150.2321-0.04440.01140.12580.04370.0609-16.113132.39070.9694
50.7840.34370.37743.33620.11411.1586-0.08920.02870.0925-0.17910.01920.4536-0.003-0.05850.070.1211-0.0184-0.0080.1304-0.00820.1821-32.08422.65090.8616
61.0165-0.53550.46592.1804-0.3851.32180.03230.1032-0.0235-0.09050.06990.03310.01610.1114-0.10230.13210.00520.02340.1943-0.02980.071-14.841-17.74910.8299
71.292-0.26770.77511.3491-0.3462.31820.0642-0.0963-0.103-0.16040.05340.21930.1938-0.1299-0.11760.10430.00720.02510.17840.00970.1258-13.0093-35.073429.5013
81.07030.22310.97740.96440.31272.55520.05670.0528-0.1051-0.13050.0232-0.13340.07450.1107-0.07980.08340.04890.07720.1567-0.02020.161710.8922-32.632741.0893
90.93080.23830.29983.19630.56921.22380.0705-0.0965-0.00210.1771-0.0228-0.14560.0566-0.073-0.04770.0505-0.01880.04590.16790.01650.146510.7086-13.68569.1868
100.9094-0.08310.10863.26640.1050.9237-0.00210.0055-0.0130.0516-0.0272-0.56760.01810.06090.02930.0186-0.00030.04860.13260.01270.28625.37118.309467.5752
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A0 - 170
2X-RAY DIFFRACTION2B0 - 170
3X-RAY DIFFRACTION3C1 - 168
4X-RAY DIFFRACTION4D0 - 170
5X-RAY DIFFRACTION5E1 - 167
6X-RAY DIFFRACTION6F0 - 169
7X-RAY DIFFRACTION7G1 - 167
8X-RAY DIFFRACTION8H0 - 169
9X-RAY DIFFRACTION9I1 - 169
10X-RAY DIFFRACTION10J0 - 169

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