[English] 日本語
Yorodumi
- PDB-2r37: Crystal structure of human glutathione peroxidase 3 (selenocystei... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2r37
TitleCrystal structure of human glutathione peroxidase 3 (selenocysteine to glycine mutant)
ComponentsGlutathione peroxidase 3
KeywordsOXIDOREDUCTASE / GLUTATHIONE / PEROXIDASE / PLASMA / STRUCTURAL GENOMICS CONSORTIUM / SGC / Secreted / Selenium / Selenocysteine
Function / homology
Function and homology information


response to lipid hydroperoxide / selenium binding / glutathione peroxidase / glutathione peroxidase activity / Detoxification of Reactive Oxygen Species / transcription factor binding / hydrogen peroxide catabolic process / peroxidase activity / cellular response to oxidative stress / extracellular space ...response to lipid hydroperoxide / selenium binding / glutathione peroxidase / glutathione peroxidase activity / Detoxification of Reactive Oxygen Species / transcription factor binding / hydrogen peroxide catabolic process / peroxidase activity / cellular response to oxidative stress / extracellular space / extracellular exosome / extracellular region / identical protein binding
Similarity search - Function
Glutathione peroxidase active site / Glutathione peroxidases active site. / Glutathione peroxidase / Glutathione peroxidase conserved site / Glutathione peroxidase / Glutathione peroxidases signature 2. / Glutathione peroxidase profile. / Glutaredoxin / Glutaredoxin / Thioredoxin-like superfamily ...Glutathione peroxidase active site / Glutathione peroxidases active site. / Glutathione peroxidase / Glutathione peroxidase conserved site / Glutathione peroxidase / Glutathione peroxidases signature 2. / Glutathione peroxidase profile. / Glutaredoxin / Glutaredoxin / Thioredoxin-like superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Glutathione peroxidase 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsPilka, E.S. / Guo, K. / Gileadi, O. / Rojkowa, A. / von Delft, F. / Pike, A.C.W. / Kavanagh, K.L. / Johannson, C. / Sundstrom, M. / Arrowsmith, C.H. ...Pilka, E.S. / Guo, K. / Gileadi, O. / Rojkowa, A. / von Delft, F. / Pike, A.C.W. / Kavanagh, K.L. / Johannson, C. / Sundstrom, M. / Arrowsmith, C.H. / Weigelt, J. / Edwards, A.M. / Oppermann, U. / Structural Genomics Consortium (SGC)
CitationJournal: TO BE PUBLISHED
Title: Crystal structure of human glutathione peroxidase 3 (selenocysteine to glycine mutant).
Authors: Pilka, E.S. / Guo, K. / Gileadi, O. / Rojkowa, A. / von Delft, F. / Pike, A.C.W. / Kavanagh, K.L. / Johannson, C. / Sundstrom, M. / Arrowsmith, C.H. / Weigelt, J. / Edwards, A.M. / Oppermann, U.
History
DepositionAug 29, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 11, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Oct 20, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / 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 / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Aug 30, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Glutathione peroxidase 3
B: Glutathione peroxidase 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,2196
Polymers47,1022
Non-polymers1174
Water7,314406
1
A: Glutathione peroxidase 3
hetero molecules

A: Glutathione peroxidase 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,2196
Polymers47,1022
Non-polymers1174
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_545-x,-y-1,z1
Buried area1890 Å2
MethodPISA
2
B: Glutathione peroxidase 3
hetero molecules

B: Glutathione peroxidase 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,2196
Polymers47,1022
Non-polymers1174
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
Buried area1870 Å2
MethodPISA
3
A: Glutathione peroxidase 3
hetero molecules

A: Glutathione peroxidase 3
hetero molecules

B: Glutathione peroxidase 3
hetero molecules

B: Glutathione peroxidase 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,43712
Polymers94,2034
Non-polymers2348
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_545-x,-y-1,z1
crystal symmetry operation3_545-x+1/2,y-1/2,-z1
crystal symmetry operation4_445x-1/2,-y-1/2,-z1
Buried area6010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)103.720, 61.308, 100.400
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
DetailsPossibly tetramer

-
Components

#1: Protein Glutathione peroxidase 3 / / GSHPx-3 / GPx-3 / Plasma glutathione peroxidase / GSHPx-P / Extracellular glutathione peroxidase / GPx-P


Mass: 23550.846 Da / Num. of mol.: 2 / Fragment: Residues 25-223 / Mutation: C73G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GPX3, GPXP / Plasmid: pNIC-CTHF / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta / References: UniProt: P22352, glutathione peroxidase
#2: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 406 / 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: 3.39 Å3/Da / Density % sol: 63.7 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 0.1M PCB pH 8.0, 60% MPD, VAPOR DIFFUSION, SITTING DROP, temperature 277K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1.00721 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Jul 15, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00721 Å / Relative weight: 1
ReflectionResolution: 1.85→38.84 Å / Num. all: 226425 / Num. obs: 226199 / % possible obs: 99.9 % / Observed criterion σ(I): 2 / Redundancy: 4.1 % / Rmerge(I) obs: 0.086 / Rsym value: 0.099 / Net I/σ(I): 12.5
Reflection shellResolution: 1.85→1.95 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.664 / Mean I/σ(I) obs: 2.3 / Num. unique all: 7975 / Rsym value: 0.763 / % possible all: 100

-
Processing

Software
NameVersionClassification
REFMAC5.3.0040refinement
MAR345CCDdata collection
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2I3Y

2i3y


Resolution: 1.85→38 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.959 / SU B: 3.906 / SU ML: 0.061 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.085 / ESU R Free: 0.088 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: The Bijvoet differences were used for phasing. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18263 2807 5.1 %RANDOM
Rwork0.1511 ---
obs0.15269 52544 99.91 %-
all-55398 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 21.621 Å2
Baniso -1Baniso -2Baniso -3
1-0.75 Å20 Å20 Å2
2---0.27 Å20 Å2
3----0.49 Å2
Refinement stepCycle: LAST / Resolution: 1.85→38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3013 0 4 406 3423
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0223140
X-RAY DIFFRACTIONr_bond_other_d0.0010.022169
X-RAY DIFFRACTIONr_angle_refined_deg1.4141.9624258
X-RAY DIFFRACTIONr_angle_other_deg1.235278
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2395377
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.12323.836146
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.51615518
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.3041515
X-RAY DIFFRACTIONr_chiral_restr0.0920.2449
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.023476
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02673
X-RAY DIFFRACTIONr_nbd_refined0.210.2570
X-RAY DIFFRACTIONr_nbd_other0.1870.22187
X-RAY DIFFRACTIONr_nbtor_refined0.1870.21533
X-RAY DIFFRACTIONr_nbtor_other0.0890.21529
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.160.2263
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.0940.28
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.0930.210
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2560.248
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1510.223
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.5231882
X-RAY DIFFRACTIONr_mcbond_other0.8463772
X-RAY DIFFRACTIONr_mcangle_it3.83453044
X-RAY DIFFRACTIONr_scbond_it6.27281307
X-RAY DIFFRACTIONr_scangle_it8.75111214
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.85→1.898 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.253 215 -
Rwork0.22 3803 -
obs--99.95 %
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)
11.23410.13780.15651.3257-0.23030.9296-0.01460.1120.0565-0.0711-0.0079-0.03750.05430.06320.0225-0.0681-0.00370.0032-0.09330.0016-0.048810.9368-13.8473-14.5525
21.26590.04830.08681.17860.46150.9814-0.12010.25240.0859-0.1250.05610.0607-0.13360.05290.0639-0.0334-0.059-0.02790.01490.0492-0.072334.996310.5121-23.43
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA38 - 22815 - 205
2X-RAY DIFFRACTION2BB36 - 22213 - 199

+
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://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