[English] 日本語
Yorodumi
- PDB-5zte: Crystal structure of PrxA C119S mutant from Arabidopsis thaliana -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5zte
TitleCrystal structure of PrxA C119S mutant from Arabidopsis thaliana
Components2-Cys peroxiredoxin BAS1, chloroplastic
KeywordsOXIDOREDUCTASE / Arabidopsis thaliana / redox regulation / chloroplast thioredoxin systems / oxidative and photo-oxidative stress.
Function / homology
Function and homology information


stromule / thioredoxin-dependent peroxiredoxin / peroxiredoxin activity / thylakoid / thioredoxin peroxidase activity / apoplast / chloroplast envelope / chloroplast stroma / response to cold / chloroplast ...stromule / thioredoxin-dependent peroxiredoxin / peroxiredoxin activity / thylakoid / thioredoxin peroxidase activity / apoplast / chloroplast envelope / chloroplast stroma / response to cold / chloroplast / cell redox homeostasis / peroxidase activity / response to oxidative stress / defense response to bacterium / cytosol
Similarity search - Function
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-Cys peroxiredoxin BAS1, chloroplastic
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.6 Å
AuthorsYang, Y. / Cai, W. / Wang, J. / Pan, W. / Liu, L. / Wang, M. / Zhang, M.
CitationJournal: Acta Crystallogr F Struct Biol Commun / Year: 2018
Title: Crystal structure of Arabidopsis thaliana peroxiredoxin A C119S mutant.
Authors: Yang, Y. / Cai, W. / Wang, J. / Pan, W. / Liu, L. / Wang, M. / Zhang, M.
History
DepositionMay 3, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 10, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 24, 2018Group: Data collection / Database references / Structure summary
Category: citation / entity / struct
Item: _citation.journal_abbrev / _citation.pdbx_database_id_PubMed ..._citation.journal_abbrev / _citation.pdbx_database_id_PubMed / _citation.title / _entity.formula_weight / _struct.title
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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: 2-Cys peroxiredoxin BAS1, chloroplastic
B: 2-Cys peroxiredoxin BAS1, chloroplastic
C: 2-Cys peroxiredoxin BAS1, chloroplastic
D: 2-Cys peroxiredoxin BAS1, chloroplastic
E: 2-Cys peroxiredoxin BAS1, chloroplastic
F: 2-Cys peroxiredoxin BAS1, chloroplastic
G: 2-Cys peroxiredoxin BAS1, chloroplastic
H: 2-Cys peroxiredoxin BAS1, chloroplastic
I: 2-Cys peroxiredoxin BAS1, chloroplastic
J: 2-Cys peroxiredoxin BAS1, chloroplastic


Theoretical massNumber of molelcules
Total (without water)229,06010
Polymers229,06010
Non-polymers00
Water9,188510
1
A: 2-Cys peroxiredoxin BAS1, chloroplastic
B: 2-Cys peroxiredoxin BAS1, chloroplastic
C: 2-Cys peroxiredoxin BAS1, chloroplastic
D: 2-Cys peroxiredoxin BAS1, chloroplastic
E: 2-Cys peroxiredoxin BAS1, chloroplastic

A: 2-Cys peroxiredoxin BAS1, chloroplastic
B: 2-Cys peroxiredoxin BAS1, chloroplastic
C: 2-Cys peroxiredoxin BAS1, chloroplastic
D: 2-Cys peroxiredoxin BAS1, chloroplastic
E: 2-Cys peroxiredoxin BAS1, chloroplastic


Theoretical massNumber of molelcules
Total (without water)229,06010
Polymers229,06010
Non-polymers00
Water18010
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Buried area27480 Å2
ΔGint-189 kcal/mol
Surface area73720 Å2
MethodPISA
2
F: 2-Cys peroxiredoxin BAS1, chloroplastic
G: 2-Cys peroxiredoxin BAS1, chloroplastic
H: 2-Cys peroxiredoxin BAS1, chloroplastic
I: 2-Cys peroxiredoxin BAS1, chloroplastic
J: 2-Cys peroxiredoxin BAS1, chloroplastic

F: 2-Cys peroxiredoxin BAS1, chloroplastic
G: 2-Cys peroxiredoxin BAS1, chloroplastic
H: 2-Cys peroxiredoxin BAS1, chloroplastic
I: 2-Cys peroxiredoxin BAS1, chloroplastic
J: 2-Cys peroxiredoxin BAS1, chloroplastic


Theoretical massNumber of molelcules
Total (without water)229,06010
Polymers229,06010
Non-polymers00
Water18010
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,y,-z1
Buried area26520 Å2
ΔGint-194 kcal/mol
Surface area72900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)124.212, 216.189, 98.449
Angle α, β, γ (deg.)90.000, 101.470, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11F-345-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and resid 73 through 259)
21(chain B and resid 73 through 259)
31(chain C and resid 73 through 259)
41(chain D and resid 73 through 259)
51(chain E and resid 73 through 259)
61(chain F and resid 73 through 259)
71chain G
81(chain H and resid 73 through 259)
91(chain I and resid 73 through 259)
101(chain J and resid 73 through 259)

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: PRO / Beg label comp-ID: PRO / End auth comp-ID: SER / End label comp-ID: SER / Auth seq-ID: 73 - 259 / Label seq-ID: 2 - 188

Dom-IDSelection detailsAuth asym-IDLabel asym-ID
1(chain A and resid 73 through 259)AA
2(chain B and resid 73 through 259)BB
3(chain C and resid 73 through 259)CC
4(chain D and resid 73 through 259)DD
5(chain E and resid 73 through 259)EE
6(chain F and resid 73 through 259)FF
7chain GGG
8(chain H and resid 73 through 259)HH
9(chain I and resid 73 through 259)II
10(chain J and resid 73 through 259)JJ

-
Components

#1: Protein
2-Cys peroxiredoxin BAS1, chloroplastic / 2-Cys peroxiredoxin A / Thiol-specific antioxidant protein A


Mass: 22905.967 Da / Num. of mol.: 10 / Mutation: C119S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: BAS1, At3g11630, F24K9.28, T19F11.3 / Plasmid: pET22b / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q96291, peroxiredoxin
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 510 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.83 Å3/Da / Density % sol: 56.5 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.24 M lithium sulfate, 0.1 M Tris-HCl pH 8.5, 26%(w/v) PEG 4000

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.9788 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jan 21, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9788 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. obs: 74467 / % possible obs: 95.9 % / Redundancy: 3.7 % / Biso Wilson estimate: 40.05 Å2 / Rmerge(I) obs: 0.127 / Rpim(I) all: 0.074 / Rrim(I) all: 0.148 / Χ2: 0.982 / Net I/σ(I): 7.2
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.6-2.693.40.97272810.6620.5891.1420.93294.1
2.69-2.83.40.73772400.7790.4490.8670.92293.9
2.8-2.933.50.51269240.8850.3080.6010.93589.3
2.93-3.083.80.35375740.9450.2050.4090.96397.5
3.08-3.283.80.26976430.9670.1550.3111.01198.3
3.28-3.533.90.17676180.9830.1010.2031.02698.5
3.53-3.883.80.12776360.9890.0740.1471.0498.4
3.88-4.453.70.08372740.9950.0490.0960.98293.4
4.45-5.640.06876810.9960.0390.0790.97299.1
5.6-503.70.05175960.9980.0290.0591.00996.6

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassification
HKL-2000data reduction
HKL-2000data scaling
PHENIXrefinement
PDB_EXTRACT3.24data extraction
MoRDaphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3QPM

3qpm


Resolution: 2.6→40.744 Å / SU ML: 0.36 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 31.17
RfactorNum. reflection% reflection
Rfree0.2439 3762 5.06 %
Rwork0.196 --
obs0.1985 74312 95.5 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 114.47 Å2 / Biso mean: 39.7711 Å2 / Biso min: 17.58 Å2
Refinement stepCycle: final / Resolution: 2.6→40.744 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15320 0 0 510 15830
Biso mean---39.02 -
Num. residues----1939
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00615682
X-RAY DIFFRACTIONf_angle_d0.81421223
X-RAY DIFFRACTIONf_chiral_restr0.0542358
X-RAY DIFFRACTIONf_plane_restr0.0062722
X-RAY DIFFRACTIONf_dihedral_angle_d10.6449355
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A9162X-RAY DIFFRACTION9.836TORSIONAL
12B9162X-RAY DIFFRACTION9.836TORSIONAL
13C9162X-RAY DIFFRACTION9.836TORSIONAL
14D9162X-RAY DIFFRACTION9.836TORSIONAL
15E9162X-RAY DIFFRACTION9.836TORSIONAL
16F9162X-RAY DIFFRACTION9.836TORSIONAL
17G9162X-RAY DIFFRACTION9.836TORSIONAL
18H9162X-RAY DIFFRACTION9.836TORSIONAL
19I9162X-RAY DIFFRACTION9.836TORSIONAL
110J9162X-RAY DIFFRACTION9.836TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 27

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.6004-2.63330.32861520.30242377252989
2.6333-2.6680.35241550.2982508266393
2.668-2.70450.37011320.28792603273595
2.7045-2.74320.33921210.29082539266093
2.7432-2.78410.34061130.28962606271995
2.7841-2.82760.34111270.26812565269293
2.8276-2.87390.29441390.25662335247487
2.8739-2.92350.2961200.25872426254689
2.9235-2.97660.32931280.24092704283297
2.9766-3.03390.28071350.2272695283098
3.0339-3.09580.29851330.21852650278397
3.0958-3.16310.24461290.22212705283498
3.1631-3.23660.29491540.2142637279198
3.2366-3.31750.29341740.20512666284098
3.3175-3.40720.27181550.19472689284498
3.4072-3.50740.24591530.19912678283199
3.5074-3.62050.24961340.19072706284099
3.6205-3.74980.24931460.18732705285198
3.7498-3.89980.23391570.17632657281498
3.8998-4.07720.19641410.15752659280097
4.0772-4.29190.19271080.15812403251187
4.2919-4.56050.18971190.14812680279998
4.5605-4.91210.19451450.14392739288499
4.9121-5.40540.17891570.16272738289599
5.4054-6.18520.23981430.18542703284699
6.1852-7.78380.2241520.19942650280297
7.7838-40.74890.17691400.16382527266791

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbjlc1.pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more