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- PDB-4kw6: Crystal structure of Peroxiredoxin-1 (C-terminal truncation mutan... -

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Basic information

Entry
Database: PDB / ID: 4kw6
TitleCrystal structure of Peroxiredoxin-1 (C-terminal truncation mutant) from the human hookworm Ancylostoma ceylanicum bound to conoidin A
ComponentsPeroxiredoxin-1
KeywordsOXIDOREDUCTASE/OXIDOREDUCTASE INHIBITOR / 2-cys peroxiredoxin / OXIDOREDUCTASE-OXIDOREDUCTASE INHIBITOR complex
Function / homology
Function and homology information


leukocyte activation / thioredoxin-dependent peroxiredoxin / thioredoxin peroxidase activity / removal of superoxide radicals / cell redox homeostasis / hydrogen peroxide catabolic process / 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
2,3-bis(bromomethyl)quinoxaline 1,4-dioxide / thioredoxin-dependent peroxiredoxin
Similarity search - Component
Biological speciesAncylostoma ceylanicum (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 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
DepositionMay 23, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 31, 2013Provider: repository / Type: Initial release
Revision 1.1Aug 14, 2013Group: Database references
Revision 1.2Sep 11, 2013Group: Database references
Revision 1.3Sep 20, 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_conn / 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_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _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

Downloads & links

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Assembly

Deposited unit
A: Peroxiredoxin-1
B: Peroxiredoxin-1
C: Peroxiredoxin-1
D: Peroxiredoxin-1
E: Peroxiredoxin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)101,8527
Polymers101,1565
Non-polymers6962
Water27015
1
A: Peroxiredoxin-1
B: Peroxiredoxin-1
C: Peroxiredoxin-1
D: Peroxiredoxin-1
E: Peroxiredoxin-1
hetero molecules

A: Peroxiredoxin-1
B: Peroxiredoxin-1
C: Peroxiredoxin-1
D: Peroxiredoxin-1
E: Peroxiredoxin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)203,70414
Polymers202,31210
Non-polymers1,3924
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_557-x,y,-z+21
Buried area18540 Å2
ΔGint-131 kcal/mol
Surface area72280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)141.554, 141.657, 68.855
Angle α, β, γ (deg.)90.00, 98.50, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
Peroxiredoxin-1 / AcePrx-1


Mass: 20231.189 Da / Num. of mol.: 5 / Fragment: UNP residues 1-171
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, peroxiredoxin
#2: Chemical ChemComp-QDO / 2,3-bis(bromomethyl)quinoxaline 1,4-dioxide / conoidin A


Mass: 347.991 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H8Br2N2O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 15 / 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: 3.37 Å3/Da / Density % sol: 63.55 %
Crystal growTemperature: 285 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 0.1 M MES, 1-2% PEG3350, 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: X25 / Wavelength: 1.1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 18, 2013
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 3→49.84 Å / Num. all: 25771 / Num. obs: 18994 / % possible obs: 74.28 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.079
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allDiffraction-ID% possible all
3-3.121.40.3231.84484116.2
3.27-3.4420.2233.361582152.8

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
REFMAC5.7.0029refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4FH8

4fh8


Resolution: 3→49.84 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.938 / SU B: 37.364 / SU ML: 0.285 / Cross valid method: THROUGHOUT / ESU R Free: 0.404 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : RESIDUAL ONLY. AUTHOR STATES THAT LIGAND QDO ON CHAIN C WAS BUILT INTO WEAK POSITIVE ELECTRON DENSITY
RfactorNum. reflection% reflectionSelection details
Rfree0.20002 1028 5.1 %RANDOM
Rwork0.18588 ---
all0.2 26458 --
obs0.18661 18994 74.28 %-
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: 92.07 Å2
Baniso -1Baniso -2Baniso -3
1--6.25 Å20 Å2-9.35 Å2
2--2.45 Å20 Å2
3---4.98 Å2
Refinement stepCycle: LAST / Resolution: 3→49.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6761 0 27 15 6803
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0196965
X-RAY DIFFRACTIONr_angle_refined_deg0.9571.9649450
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.9895851
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.63524.006312
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.827151137
X-RAY DIFFRACTIONr_dihedral_angle_4_deg7.1281530
X-RAY DIFFRACTIONr_chiral_restr0.0710.21046
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0215305
X-RAY DIFFRACTIONr_rigid_bond_restr3.69936964
X-RAY DIFFRACTIONr_sphericity_free26.09511
X-RAY DIFFRACTIONr_sphericity_bonded16.60256792
LS refinement shellResolution: 3→3.078 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.313 10 -
Rwork0.436 267 -
obs--14 %
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)
13.8714-0.07711.02582.07640.08243.9753-0.0656-0.2355-0.73420.32280.1001-0.08060.5411-0.0408-0.03450.35580.11470.23440.15990.21490.5013-2.4788-68.394183.7399
22.2471.0680.57314.70661.38384.4852-0.023-0.0084-0.46560.30220.1143-0.36270.20980.2159-0.09130.18440.18580.12780.20830.10820.348820.3323-55.405683.3692
33.5826-0.25040.0126.1290.82992.7193-0.1732-0.6323-0.06220.90920.2452-0.30290.02040.1876-0.0720.48010.10280.02850.36280.06590.045419.2398-25.8475100.6443
45.9422-2.31230.37826.7445-0.44962.8153-0.2949-0.3680.32780.45380.2557-0.6902-0.18090.30710.03920.1585-0.1146-0.0150.2237-0.06540.081922.6298-5.032384.9341
57.0191-1.11780.68973.0066-0.50392.66290.0833-0.37740.72410.2049-0.0178-0.0604-0.2794-0.0871-0.06540.2904-0.05630.11930.0581-0.07470.1311-6.06313.696680.5115
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A0 - 171
2X-RAY DIFFRACTION2B0 - 170
3X-RAY DIFFRACTION3C1 - 170
4X-RAY DIFFRACTION4D0 - 171
5X-RAY DIFFRACTION5E1 - 171

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