[English] 日本語
Yorodumi
- PDB-4k1f: Crystal structure of reduced tryparedoxin peroxidase from leishma... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4k1f
TitleCrystal structure of reduced tryparedoxin peroxidase from leishmania major at 2.34 A resolution
ComponentsTryparedoxin peroxidase
KeywordsOXIDOREDUCTASE / Thioredoxin fold / PEROXIDASE
Function / homology
Function and homology information


thioredoxin-dependent peroxiredoxin / peroxiredoxin activity / thioredoxin peroxidase activity / cell redox homeostasis / hydrogen peroxide catabolic process / cilium / response to oxidative stress / nucleoplasm / cytoplasm / 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 / 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
3,6,9,12,15,18,21-HEPTAOXATRICOSANE-1,23-DIOL / DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / thioredoxin-dependent peroxiredoxin
Similarity search - Component
Biological speciesLeishmania major (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.34 Å
AuthorsIlari, A. / Fiorillo, A. / Di Chiaro, F.
CitationJournal: Sci Rep / Year: 2015
Title: Structure-based discovery of the first non-covalent inhibitors of Leishmania major tryparedoxin peroxidase by high throughput docking
Authors: Brindisi, M. / Brogi, S. / Relitti, N. / Vallone, A. / Butini, S. / Gemma, S. / Novellino, E. / Colotti, G. / Angiulli, G. / Di Chiaro, F. / Fiorillo, A. / Ilari, A. / Campiani, G.
History
DepositionApr 5, 2013Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 9, 2014Provider: repository / Type: Initial release
Revision 1.1Jul 30, 2014Group: Data collection
Revision 1.2Jun 10, 2015Group: Database references
Revision 1.3Nov 8, 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_ncs_dom_lim / 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_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 / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Tryparedoxin peroxidase
B: Tryparedoxin peroxidase
C: Tryparedoxin peroxidase
D: Tryparedoxin peroxidase
E: Tryparedoxin peroxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)111,89415
Polymers110,8075
Non-polymers1,08710
Water6,125340
1
A: Tryparedoxin peroxidase
B: Tryparedoxin peroxidase
C: Tryparedoxin peroxidase
D: Tryparedoxin peroxidase
E: Tryparedoxin peroxidase
hetero molecules

A: Tryparedoxin peroxidase
B: Tryparedoxin peroxidase
C: Tryparedoxin peroxidase
D: Tryparedoxin peroxidase
E: Tryparedoxin peroxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)223,78830
Polymers221,61410
Non-polymers2,17420
Water18010
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
Buried area34710 Å2
ΔGint-206 kcal/mol
Surface area69140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)111.811, 226.203, 91.719
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
51E

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: TRP / Beg label comp-ID: TRP / End auth comp-ID: TRP / End label comp-ID: TRP / Refine code: 5 / Auth seq-ID: 38 - 177 / Label seq-ID: 38 - 177

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB
3CC
4DD
5EE

-
Components

-
Protein , 1 types, 5 molecules ABCDE

#1: Protein
Tryparedoxin peroxidase


Mass: 22161.408 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Leishmania major (eukaryote) / Gene: TRYP3 / Plasmid: peT22b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q4QF76, peroxiredoxin

-
Non-polymers , 5 types, 350 molecules

#2: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#4: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H10O3
#5: Chemical ChemComp-PE8 / 3,6,9,12,15,18,21-HEPTAOXATRICOSANE-1,23-DIOL


Mass: 370.436 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H34O9
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 340 / 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: 2.63 Å3/Da / Density % sol: 53.28 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 20% PEG 3350, 0.2M NaSO4, 0.1M TRIS-HCl, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 294K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 5.2R / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Mar 14, 2013
RadiationMonochromator: Double Crystal Si111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.34→113.1 Å / Num. all: 49646 / Num. obs: 49113 / % possible obs: 98.9 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 41.222 Å2 / Rmerge(I) obs: 0.162 / Net I/σ(I): 10.26
Reflection shell

Rmerge(I) obs: 1.07 / Diffraction-ID: 1

Resolution (Å)Rmerge F obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) all% possible all
2.34-2.480.7121.6541117791775001.18994.7
2.48-2.650.8182.5142092744174310.82599.9
2.65-2.860.8633.2537406696569410.66599.7
2.86-3.130.9495.7435518641264010.35899.8
3.13-3.50.98410.9733339582458190.18299.9
3.5-4.040.99216.8227189517851600.11499.7
4.04-4.940.99625.4923653439743840.0799.7
4.94-6.940.99623.218855346934540.07499.6
6.94-113.10.99935.0910455204320230.04199

-
Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation3.5 Å43.98 Å
Translation3.5 Å43.98 Å

-
Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACT3.11data extraction
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3TUE

3tue


Resolution: 2.34→113.1 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.913 / WRfactor Rfree: 0.2467 / WRfactor Rwork: 0.1936 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.8549 / SU B: 6.663 / SU ML: 0.16 / SU R Cruickshank DPI: 0.3519 / SU Rfree: 0.246 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.352 / ESU R Free: 0.246 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2467 2489 5.1 %RANDOM
Rwork0.1936 ---
obs0.1963 49112 98.91 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 65.65 Å2 / Biso mean: 27.4724 Å2 / Biso min: 11.12 Å2
Baniso -1Baniso -2Baniso -3
1-0.05 Å20 Å20 Å2
2--0.52 Å20 Å2
3----0.56 Å2
Refinement stepCycle: LAST / Resolution: 2.34→113.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7711 0 67 340 8118
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0227993
X-RAY DIFFRACTIONr_angle_refined_deg1.531.96910789
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3565992
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.49324.461343
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.816151370
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.6751535
X-RAY DIFFRACTIONr_chiral_restr0.1030.21157
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0216015
X-RAY DIFFRACTIONr_mcbond_it0.6531.54930
X-RAY DIFFRACTIONr_mcangle_it1.22927961
X-RAY DIFFRACTIONr_scbond_it2.00933063
X-RAY DIFFRACTIONr_scangle_it3.3014.52823
Refine LS restraints NCS

Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A560MEDIUM POSITIONAL0.120.5
2B560MEDIUM POSITIONAL0.110.5
3C560MEDIUM POSITIONAL0.120.5
4D560MEDIUM POSITIONAL0.120.5
5E560MEDIUM POSITIONAL0.120.5
1A556LOOSE POSITIONAL0.375
2B556LOOSE POSITIONAL0.355
3C556LOOSE POSITIONAL0.345
4D556LOOSE POSITIONAL0.385
5E556LOOSE POSITIONAL0.375
1A560MEDIUM THERMAL1.532
2B560MEDIUM THERMAL0.962
3C560MEDIUM THERMAL0.792
4D560MEDIUM THERMAL0.792
5E560MEDIUM THERMAL0.962
1A556LOOSE THERMAL1.5610
2B556LOOSE THERMAL1.2310
3C556LOOSE THERMAL1.1210
4D556LOOSE THERMAL1.1210
5E556LOOSE THERMAL1.1610
LS refinement shellResolution: 2.336→2.397 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.276 180 -
Rwork0.221 3087 -
all-3267 -
obs--90.35 %

+
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://pdbjlvh1.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