[English] 日本語
Yorodumi
- PDB-3ish: Crystal structure of Helicobacter pylori thioredoxin reductase -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3ish
TitleCrystal structure of Helicobacter pylori thioredoxin reductase
ComponentsThioredoxin reductase
KeywordsOXIDOREDUCTASE / Disulfide bond / FAD / Flavoprotein / NADP / Redox-active center
Function / homology
Function and homology information


thioredoxin-disulfide reductase / thioredoxin-disulfide reductase (NADPH) activity / removal of superoxide radicals / cell redox homeostasis / cytoplasm
Similarity search - Function
Thioredoxin reductase / Pyridine nucleotide-disulphide oxidoreductase, class-II, active site / Pyridine nucleotide-disulphide oxidoreductases class-II active site. / FAD/NAD(P)-binding domain / Pyridine nucleotide-disulphide oxidoreductase / FAD/NAD(P)-binding domain / FAD/NAD(P)-binding domain / 3-Layer(bba) Sandwich / FAD/NAD(P)-binding domain superfamily / Alpha Beta
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / Thioredoxin reductase
Similarity search - Component
Biological speciesHelicobacter pylori (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.43 Å
AuthorsSanders, D. / Obiero, J. / van Straaten, K.
CitationJournal: To be Published
Title: Crystal structure of Helicobacter pylori thioredoxin reductase
Authors: Sanders, D. / Obiero, J. / van Straaten, K.
History
DepositionAug 25, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 6, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Sep 6, 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_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_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: Thioredoxin reductase
B: Thioredoxin reductase
C: Thioredoxin reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,0886
Polymers100,7323
Non-polymers2,3573
Water8,917495
1
A: Thioredoxin reductase
B: Thioredoxin reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,7264
Polymers67,1552
Non-polymers1,5712
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4350 Å2
ΔGint-24 kcal/mol
Surface area26740 Å2
MethodPISA
2
C: Thioredoxin reductase
hetero molecules

C: Thioredoxin reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,7264
Polymers67,1552
Non-polymers1,5712
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555x-y,-y,-z+1/31
Buried area4570 Å2
ΔGint-25 kcal/mol
Surface area26790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.400, 89.400, 279.900
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11B
21A
31C

NCS domain segments:

Ens-ID: 1 / Refine code: 3

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11METMETGLUGLUBB1 - 321 - 32
21METMETGLUGLUAA1 - 321 - 32
31METMETGLUGLUCC1 - 321 - 32
12LYSLYSSERSERBB33 - 8933 - 89
22LYSLYSSERSERAA33 - 8933 - 89
32LYSLYSSERSERCC33 - 8933 - 89
13HISHISILEILEBB90 - 11990 - 119
23HISHISILEILEAA90 - 11990 - 119
33HISHISILEILECC90 - 11990 - 119
14CYSCYSTYRTYRBB133 - 141133 - 141
24CYSCYSTYRTYRAA133 - 141133 - 141
34CYSCYSTYRTYRCC133 - 141133 - 141
15VALVALGLYGLYBB146 - 150146 - 150
25VALVALGLYGLYAA146 - 150146 - 150
35VALVALGLYGLYCC146 - 150146 - 150
16VALVALARGARGBB156 - 174156 - 174
26VALVALARGARGAA156 - 174156 - 174
36VALVALARGARGCC156 - 174156 - 174
17ILEILEGLUGLUBB194 - 204194 - 204
27ILEILEGLUGLUAA194 - 204194 - 204
37ILEILEGLUGLUCC194 - 204194 - 204
18LYSLYSHISHISBB225 - 311225 - 311
28LYSLYSHISHISAA225 - 311225 - 311
38LYSLYSHISHISCC225 - 311225 - 311

-
Components

#1: Protein Thioredoxin reductase / / TRXR


Mass: 33577.273 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Helicobacter pylori (bacteria) / Strain: 26695 / Gene: HP0825 / Plasmid: pROK1 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta / References: UniProt: P56431
#2: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE / Flavin adenine dinucleotide


Mass: 785.550 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 495 / 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: 3.21 Å3/Da / Density % sol: 61.63 %
Crystal growTemperature: 277 K / pH: 5.6
Details: 2.0 M Ammonium sulfate,0.2M Ammonium Nitrate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 277K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.97
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jan 31, 2007 / Details: MIRRORS
RadiationMonochromator: SAGITALLY FOCUSED SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 2.43→19.98 Å / Num. obs: 49803 / Observed criterion σ(I): -2 / Redundancy: 10.5 % / Rmerge(I) obs: 0.068 / Rsym value: 0.068 / Net I/σ(I): 24.31

-
Processing

Software
NameVersionClassification
XDSdata scaling
MrBUMP& molrepphasing
REFMAC5refinement
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2A87

2a87


Resolution: 2.43→19.98 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.905 / SU B: 13.923 / SU ML: 0.179 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.305 / ESU R Free: 0.252 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.252 2490 5 %RANDOM
Rwork0.178 ---
obs0.181 47307 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 39.07 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å20 Å2
2--0.01 Å20 Å2
3----0.01 Å2
Refinement stepCycle: LAST / Resolution: 2.43→19.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7061 0 159 495 7715
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0260.0227373
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.4021.9829978
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2175930
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.26524.751301
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.942151235
X-RAY DIFFRACTIONr_dihedral_angle_4_deg24.3481528
X-RAY DIFFRACTIONr_chiral_restr0.1890.21098
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.025480
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2630.23429
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3170.24873
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2320.2505
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2230.282
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2480.224
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.2461.54724
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.06327341
X-RAY DIFFRACTIONr_scbond_it3.40133236
X-RAY DIFFRACTIONr_scangle_it5.3464.52637
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

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

Dom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1B996tight positional0.170.05
2A996tight positional0.230.05
3C996tight positional0.130.05
1B896loose positional0.75
2A896loose positional0.745
3C896loose positional0.665
1B996tight thermal0.40.5
2A996tight thermal0.340.5
3C996tight thermal0.550.5
1B896loose thermal3.3710
2A896loose thermal2.910
3C896loose thermal4.1710
LS refinement shellResolution: 2.43→2.49 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.299 176 -
Rwork0.212 3352 -
obs--100 %
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)
10.0471-0.02260.12090.05390.02250.461-0.00770.02150.00310.0258-0.00130.0270.04460.01460.0090.0013-0.03130.0029-0.03410.0063-0.0007-33.019-8.231211.0152
20.2034-0.0094-0.06660.16450.06450.22730.02180.050.02910.0459-0.03830.0016-0.0019-0.01530.0164-0.0124-0.0282-0.017-0.04450.0189-0.0316-33.3273-0.8533.9284
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 115
2X-RAY DIFFRACTION1B1 - 115
3X-RAY DIFFRACTION1C1 - 115
4X-RAY DIFFRACTION1A239 - 311
5X-RAY DIFFRACTION1B239 - 311
6X-RAY DIFFRACTION1C239 - 311
7X-RAY DIFFRACTION2A116 - 238
8X-RAY DIFFRACTION2B116 - 238
9X-RAY DIFFRACTION2C116 - 238

+
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