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- PDB-6j13: Redox protein from Chlamydomonas reinhardtii -

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Basic information

Entry
Database: PDB / ID: 6j13
TitleRedox protein from Chlamydomonas reinhardtii
Components2-cys peroxiredoxin
KeywordsOXIDOREDUCTASE / Peroxiredoxin / redox- / Chlamydomonas reinhardtii
Function / homology
Function and homology information


thioredoxin-dependent peroxiredoxin / peroxiredoxin activity / cell redox homeostasis / peroxidase 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
Biological speciesChlamydomonas reinhardtii (plant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsCharoenwattansatien, R. / Zinzius, K. / Tanaka, H. / Hippler, M. / Kurisu, G.
Funding support Japan, 1items
OrganizationGrant numberCountry
Ministry of Education, Culture, Sports, Science and Technology (Japan)16H06560 Japan
CitationJournal: J.Biol.Chem. / Year: 2020
Title: Calcium sensing via EF-hand 4 enables thioredoxin activity in the sensor-responder protein calredoxin in the green algaChlamydomonas reinhardtii.
Authors: Charoenwattanasatien, R. / Zinzius, K. / Scholz, M. / Wicke, S. / Tanaka, H. / Brandenburg, J.S. / Marchetti, G.M. / Ikegami, T. / Matsumoto, T. / Oda, T. / Sato, M. / Hippler, M. / Kurisu, G.
History
DepositionDec 27, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 4, 2019Provider: repository / Type: Initial release
Revision 1.1Apr 1, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 22, 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: 2-cys peroxiredoxin
B: 2-cys peroxiredoxin
C: 2-cys peroxiredoxin
D: 2-cys peroxiredoxin
E: 2-cys peroxiredoxin
F: 2-cys peroxiredoxin
G: 2-cys peroxiredoxin
H: 2-cys peroxiredoxin
I: 2-cys peroxiredoxin
J: 2-cys peroxiredoxin


Theoretical massNumber of molelcules
Total (without water)246,92810
Polymers246,92810
Non-polymers00
Water1,67593
1
A: 2-cys peroxiredoxin
B: 2-cys peroxiredoxin
C: 2-cys peroxiredoxin
D: 2-cys peroxiredoxin
E: 2-cys peroxiredoxin

A: 2-cys peroxiredoxin
B: 2-cys peroxiredoxin
C: 2-cys peroxiredoxin
D: 2-cys peroxiredoxin
E: 2-cys peroxiredoxin


Theoretical massNumber of molelcules
Total (without water)246,92810
Polymers246,92810
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_855-x+3,y,-z+1/21
Buried area17500 Å2
ΔGint-112 kcal/mol
Surface area66940 Å2
MethodPISA
2
F: 2-cys peroxiredoxin
G: 2-cys peroxiredoxin
H: 2-cys peroxiredoxin
I: 2-cys peroxiredoxin
J: 2-cys peroxiredoxin

F: 2-cys peroxiredoxin
G: 2-cys peroxiredoxin
H: 2-cys peroxiredoxin
I: 2-cys peroxiredoxin
J: 2-cys peroxiredoxin


Theoretical massNumber of molelcules
Total (without water)246,92810
Polymers246,92810
Non-polymers00
Water18010
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_855-x+3,y,-z+1/21
Buried area17520 Å2
ΔGint-113 kcal/mol
Surface area68040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)134.990, 419.230, 94.530
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein
2-cys peroxiredoxin / Peroxiredoxin / Thioredoxin peroxidase


Mass: 24692.783 Da / Num. of mol.: 10 / Fragment: UNP residues 38-235 / Mutation: C210S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chlamydomonas reinhardtii (plant) / Gene: thioredoxin peroxidase / Plasmid: PET22b / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21
References: UniProt: Q9FE86, Oxidoreductases; Acting on a peroxide as acceptor; Peroxidases
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 93 / 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: 2.93 Å3/Da / Density % sol: 58.05 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.6 / Details: PEG 3350, Sodium thiocyanate, HEPES

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Jun 7, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2.4→47.37 Å / Num. obs: 103254 / % possible obs: 98.9 % / Redundancy: 3.69 % / CC1/2: 0.994 / Rmerge(I) obs: 0.111 / Net I/σ(I): 6.72
Reflection shellResolution: 2.4→2.45 Å / Redundancy: 1.96 % / Rmerge(I) obs: 0.972 / Mean I/σ(I) obs: 1.51 / Num. unique obs: 7647 / CC1/2: 0.742 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1QMV

1qmv


Resolution: 2.4→47.37 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.947 / SU B: 19.128 / SU ML: 0.194 / Cross valid method: THROUGHOUT / ESU R: 0.278 / ESU R Free: 0.223 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2508 5201 5 %RANDOM
Rwork0.21529 ---
obs0.21706 98805 98.98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 55.068 Å2
Baniso -1Baniso -2Baniso -3
1--1.47 Å20 Å20 Å2
2---1.54 Å20 Å2
3---3.01 Å2
Refinement stepCycle: 1 / Resolution: 2.4→47.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12904 0 0 93 12997
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.01313186
X-RAY DIFFRACTIONr_bond_other_d0.0010.01712214
X-RAY DIFFRACTIONr_angle_refined_deg1.9131.63917882
X-RAY DIFFRACTIONr_angle_other_deg1.3521.57528261
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.8951623
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.82923.294686
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.255152197
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.7661560
X-RAY DIFFRACTIONr_chiral_restr0.0880.21722
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0214777
X-RAY DIFFRACTIONr_gen_planes_other0.0020.022851
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.9292.7976519
X-RAY DIFFRACTIONr_mcbond_other1.9252.7976518
X-RAY DIFFRACTIONr_mcangle_it3.1614.1868133
X-RAY DIFFRACTIONr_mcangle_other3.1614.1878134
X-RAY DIFFRACTIONr_scbond_it2.1473.0466667
X-RAY DIFFRACTIONr_scbond_other2.1473.0476668
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.5724.4629749
X-RAY DIFFRACTIONr_long_range_B_refined5.09831.54713771
X-RAY DIFFRACTIONr_long_range_B_other5.09931.52413756
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.4→2.462 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.374 384 -
Rwork0.377 7296 -
obs--99.81 %
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)
11.5433-0.3373-0.27130.57230.12860.3134-0.00030.167-0.0739-0.0219-0.01820.0786-0.04140.00290.01850.2109-0.0194-0.01910.3312-0.01490.2714217.37865.12715.742
20.7496-0.1079-0.40551.26540.21960.43530.0235-0.0784-0.22940.0798-0.0169-0.1199-0.0175-0.0358-0.00660.215-0.0017-0.02520.240.03720.3905237.66551.28229.986
30.60210.36180.17442.87110.65440.4528-0.10710.00310.0124-0.19020.1076-0.26510.0798-0.0131-0.00050.2295-0.00930.04080.0895-0.00340.5438246.60822.09715.603
41.86250.9865-0.14372.65510.43320.1668-0.0306-0.1554-0.15110.4205-0.0815-0.1270.14330.00990.11210.4078-0.01530.03080.0390.03930.4377239.278-0.33830.754
52.64580.62520.24110.61140.13480.4743-0.450.3133-0.26080.06330.1762-0.0722-0.0389-00.27370.3839-0.05290.2760.0747-0.08660.5843214.836-18.26816.625
62.4193-0.2728-0.39210.8246-0.20090.3812-0.0539-0.26550.5-0.03660.0165-0.10340.0991-0.01880.03730.27760.0102-0.01180.2007-0.07850.3548214.792-49.2830.704
71.4832-1.13680.01031.51720.48310.49370.13070.17460.2608-0.1673-0.0896-0.124-0.00730.0089-0.04110.34980.05160.04720.28960.04060.1559239.145-67.51416.101
80.38860.0672-0.36912.05810.56870.7660.0194-0.0473-0.04710.10040.0341-0.1663-0.0273-0.0042-0.05350.31490.011-0.01840.3181-0.00810.1267246.73-89.37231.814
90.75680.41280.46131.3920.13670.5178-0.00970.0047-0.0449-0.08510.055-0.0922-0.0511-0.0275-0.04540.28180.0124-0.00370.34320.00720.1469237.56-118.76617.494
101.46560.22960.35080.92710.41890.4706-0.022-0.1457-0.18320.04510.0266-0.0164-0.036-0.0267-0.00460.23980.0175-0.00070.37790.01090.1578217.475-132.62231.591
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A7 - 169
2X-RAY DIFFRACTION2B7 - 169
3X-RAY DIFFRACTION3C7 - 169
4X-RAY DIFFRACTION4D7 - 169
5X-RAY DIFFRACTION5E7 - 168
6X-RAY DIFFRACTION6F7 - 169
7X-RAY DIFFRACTION7G7 - 169
8X-RAY DIFFRACTION8H7 - 170
9X-RAY DIFFRACTION9I7 - 169
10X-RAY DIFFRACTION10J7 - 170

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