[English] 日本語
Yorodumi
- PDB-3hvv: Escherichia coli Thiol peroxidase (Tpx) peroxidatic cysteine to s... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3hvv
TitleEscherichia coli Thiol peroxidase (Tpx) peroxidatic cysteine to serine mutant (C61S)
ComponentsThiol peroxidase
KeywordsOXIDOREDUCTASE / Tpx / peroxiredoxin / peroxidase / Antioxidant
Function / homology
Function and homology information


hydroperoxide reductase activity / thioredoxin-dependent peroxiredoxin / thioredoxin peroxidase activity / cellular response to oxidative stress / periplasmic space / cytosol
Similarity search - Function
Thiol peroxidase Tpx / Thiol peroxidase conserved site / Tpx family signature. / : / Redoxin / Redoxin / Thioredoxin domain profile. / Thioredoxin domain / Glutaredoxin / Glutaredoxin ...Thiol peroxidase Tpx / Thiol peroxidase conserved site / Tpx family signature. / : / Redoxin / Redoxin / Thioredoxin domain profile. / Thioredoxin domain / Glutaredoxin / Glutaredoxin / Thioredoxin-like superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesEscherichia coli K-12 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsHall, A. / Sankaran, B. / Karplus, P.A.
CitationJournal: J.Mol.Biol. / Year: 2009
Title: Structural changes common to catalysis in the Tpx peroxiredoxin subfamily.
Authors: Hall, A. / Sankaran, B. / Poole, L.B. / Karplus, P.A.
History
DepositionJun 16, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 20, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 13, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.3Sep 6, 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: Thiol peroxidase


Theoretical massNumber of molelcules
Total (without water)17,7011
Polymers17,7011
Non-polymers00
Water5,278293
1
A: Thiol peroxidase

A: Thiol peroxidase


Theoretical massNumber of molelcules
Total (without water)35,4022
Polymers35,4022
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555-x,-x+y,-z+1/31
Buried area1510 Å2
ΔGint-12 kcal/mol
Surface area13980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.535, 59.535, 73.323
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

-
Components

#1: Protein Thiol peroxidase / Scavengase P20


Mass: 17700.953 Da / Num. of mol.: 1 / Mutation: C61S
Source method: isolated from a genetically manipulated source
Details: See Baker and Poole, 2003. / Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Strain: K-12 (XL-1 Blue) / Gene: b1324, JW1317, tpx, yzzJ / Plasmid: pPROK1 / Production host: Escherichia coli (E. coli) / Strain (production host): XL-1 Blue / References: UniProt: P0A862, peroxiredoxin
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 293 / 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: 2.12 Å3/Da / Density % sol: 41.96 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop
Details: 22% (w/v) PEG 8000, 0.05 M potassium phosphate, VAPOR DIFFUSION, HANGING DROP, temperature 277K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 0.978 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Aug 21, 2008
RadiationMonochromator: Single crystal, cylindrically bent Si(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 1.75→42 Å / Num. obs: 13755 / % possible obs: 92.8 % / Redundancy: 7.7 % / Rsym value: 0.056 / Net I/σ(I): 26.5
Reflection shellResolution: 1.75→1.84 Å / Redundancy: 4.5 % / Mean I/σ(I) obs: 3.2 / Num. unique all: 1403 / Rsym value: 0.457 / % possible all: 63.1

-
Processing

Software
NameVersionClassification
MOLREPv9.2phasing
REFMAC5.5.0046refinement
HKL-2000data reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: chain A of pdb entry 3HVS

3hvs


Resolution: 1.75→42 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.953 / SU B: 5.667 / SU ML: 0.079 / Cross valid method: THROUGHOUT / ESU R: 0.113 / ESU R Free: 0.12 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19526 714 4.9 %RANDOM
Rwork0.13625 ---
obs0.13912 13755 92.76 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 8.581 Å2
Baniso -1Baniso -2Baniso -3
1--0.97 Å2-0.48 Å20 Å2
2---0.97 Å20 Å2
3---1.45 Å2
Refinement stepCycle: LAST / Resolution: 1.75→42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1298 0 0 293 1591
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.0221277
X-RAY DIFFRACTIONr_bond_other_d0.0020.02818
X-RAY DIFFRACTIONr_angle_refined_deg1.7571.9561741
X-RAY DIFFRACTIONr_angle_other_deg1.04832015
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4615168
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.24425.45555
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.10515204
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.565156
X-RAY DIFFRACTIONr_chiral_restr0.120.2213
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.021452
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02246
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_it2.0212837
X-RAY DIFFRACTIONr_mcbond_other0.7472339
X-RAY DIFFRACTIONr_mcangle_it2.83631352
X-RAY DIFFRACTIONr_scbond_it2.7642440
X-RAY DIFFRACTIONr_scangle_it4.1743389
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.75→1.796 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.325 35 -
Rwork0.233 609 -
obs--57.65 %
Refinement TLS params.Method: refined / Origin x: -19.408 Å / Origin y: 5.644 Å / Origin z: 6.295 Å
111213212223313233
T0.0602 Å20.0024 Å2-0.0311 Å2-0.0157 Å20.0043 Å2--0.1164 Å2
L2.072 °21.3971 °20.7708 °2-2.0147 °20.71 °2--1.4775 °2
S0.1001 Å °0.0095 Å °-0.369 Å °0.0939 Å °0.0651 Å °-0.3004 Å °0.1538 Å °-0.0712 Å °-0.1652 Å °

+
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