[English] 日本語
Yorodumi
- PDB-9f65: Crystal structure of thiol peroxidase mutant (C94A) in complex wi... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9f65
TitleCrystal structure of thiol peroxidase mutant (C94A) in complex with Metro-P3* (H. pylori)
ComponentsThiol peroxidase
KeywordsOXIDOREDUCTASE / Stress Response / Detoxification / Active Site Analysis / Protein Inhibitor Interactions / Catalysis / Drug Target
Function / homology
Function and homology information


thioredoxin-dependent peroxiredoxin / thioredoxin peroxidase activity
Similarity search - Function
Thiol peroxidase Tpx / Thiol peroxidase conserved site / Tpx family signature. / : / Redoxin / Redoxin / Thioredoxin domain profile. / Thioredoxin domain / Thioredoxin-like superfamily
Similarity search - Domain/homology
: / Thiol peroxidase
Similarity search - Component
Biological speciesHelicobacter pylori (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsFiedler, M.K. / Gong, R. / Fuchs, S. / Rox, K. / Friedrich, V. / Pfeiffer, D. / Reinhardt, T. / Mibus, C. / Huber, M. / Hess, C. ...Fiedler, M.K. / Gong, R. / Fuchs, S. / Rox, K. / Friedrich, V. / Pfeiffer, D. / Reinhardt, T. / Mibus, C. / Huber, M. / Hess, C. / Mejias-Luque, R. / Gerhard, M. / Groll, M. / Sieber, S.A.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG)SFB 1309 - 325871075 Germany
CitationJournal: to be published
Title: 5-Nitroimidazole ethers boost anti-Helicobacter pylori activity via a dual mode of action and effectively eradicate infections in vivo
Authors: Fiedler, M.K. / Gong, R. / Fuchs, S. / Rox, K. / Friedrich, V. / Pfeiffer, D. / Reinhardt, T. / Mibus, C. / Huber, M. / Hess, C. / Mejias-Luque, R. / Gerhard, M. / Groll, M. / Sieber, S.A.
History
DepositionApr 30, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 14, 2025Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Thiol peroxidase
B: Thiol peroxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,5793
Polymers41,4142
Non-polymers1651
Water32418
1
A: Thiol peroxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,8722
Polymers20,7071
Non-polymers1651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Thiol peroxidase


Theoretical massNumber of molelcules
Total (without water)20,7071
Polymers20,7071
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)40.570, 67.760, 64.030
Angle α, β, γ (deg.)90.00, 98.70, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein Thiol peroxidase / Tpx / Peroxiredoxin tpx / Prx / Thioredoxin peroxidase / Thioredoxin-dependent peroxiredoxin


Mass: 20706.918 Da / Num. of mol.: 2 / Mutation: C94A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Helicobacter pylori (bacteria) / Gene: tpx, HP_0390 / Production host: Escherichia coli (E. coli)
References: UniProt: O25151, thioredoxin-dependent peroxiredoxin
#2: Chemical ChemComp-A1IAR / 3-methyl-2-(prop-2-ynoxymethyl)imidazol-4-amine


Mass: 165.192 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H11N3O / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 18 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.1 Å3/Da / Density % sol: 41.29 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 0.1 M BISTRIS, 28% PEG 2000MM

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.87313 Å
DetectorType: DECTRIS EIGER2 S 9M / Detector: PIXEL / Date: Jul 24, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.87313 Å / Relative weight: 1
ReflectionResolution: 1.95→30 Å / Num. obs: 24146 / % possible obs: 96.2 % / Redundancy: 2.9 % / Rmerge(I) obs: 0.043 / Net I/σ(I): 11.8
Reflection shellResolution: 1.95→2.05 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.638 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 3359 / % possible all: 96.7

-
Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
XSCALEdata scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.95→30 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.958 / SU B: 10.777 / SU ML: 0.129 / Cross valid method: THROUGHOUT / ESU R Free: 0.146 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21651 1207 5 %RANDOM
Rwork0.17709 ---
obs0.17903 22932 96.16 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 55.3 Å2
Baniso -1Baniso -2Baniso -3
1--5.32 Å20 Å22.12 Å2
2--2.88 Å20 Å2
3---1.71 Å2
Refinement stepCycle: 1 / Resolution: 1.95→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2570 0 0 18 2588
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.0132607
X-RAY DIFFRACTIONr_bond_other_d0.0010.0162633
X-RAY DIFFRACTIONr_angle_refined_deg1.2411.6393512
X-RAY DIFFRACTIONr_angle_other_deg1.1361.5946067
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.35328
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.22924.828116
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.66715493
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.016158
X-RAY DIFFRACTIONr_chiral_restr0.0480.2322
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022933
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02552
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_it3.4664.891318
X-RAY DIFFRACTIONr_mcbond_other3.4554.8871317
X-RAY DIFFRACTIONr_mcangle_it4.5637.3261644
X-RAY DIFFRACTIONr_mcangle_other4.577.331645
X-RAY DIFFRACTIONr_scbond_it3.3965.4061289
X-RAY DIFFRACTIONr_scbond_other3.3825.4051289
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.4467.8971868
X-RAY DIFFRACTIONr_long_range_B_refined5.42156.1822643
X-RAY DIFFRACTIONr_long_range_B_other5.43756.2152643
X-RAY DIFFRACTIONr_rigid_bond_restr0.96335240
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.95→2 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.317 89 -
Rwork0.315 1686 -
obs--96.99 %
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)
10.4546-0.01730.0430.36180.00440.5831-0.0060.0121-0.0041-0.0233-0.00670.0050.0087-0.00480.01270.10440.0019-0.02830.05310.00890.0110.9942-2.8777-28.1421
20.5004-0.0707-0.17930.51120.06410.78780.0114-0.0377-0.01410.0678-0.009-0.0260.00620.0241-0.00240.11040.0129-0.01970.06040.00620.005214.2509-0.53022.2637
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 166
2X-RAY DIFFRACTION2B2 - 166

+
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