[English] 日本語
Yorodumi
- PDB-3ia1: Crystal structure of thio-disulfide isomerase from Thermus thermo... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3ia1
TitleCrystal structure of thio-disulfide isomerase from Thermus thermophilus
ComponentsThio-disulfide isomerase/thioredoxin
KeywordsOXIDOREDUCTASE / DISULFIDE ISOMERASE / PSI-2 / NYSGXRC / STRUCTURAL GENOMICS / PROTEIN STRUCTURE INITIATIVE / NEW YORK SGX RESEARCH CENTER FOR STRUCTURAL GENOMICS
Function / homology
Function and homology information


antioxidant activity / isomerase activity / oxidoreductase activity
Similarity search - Function
: / 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
ACETATE ION / Thio-disulfide isomerase/thioredoxin
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.76 Å
AuthorsPatskovsky, Y. / Toro, R. / Freeman, J. / Chang, S. / Sauder, J.M. / Burley, S.K. / Almo, S.C. / New York SGX Research Center for Structural Genomics (NYSGXRC)
CitationJournal: To be Published
Title: Crystal structure of thio-disulfide isomerase from Thermus thermophilus
Authors: Patskovsky, Y. / Toro, R. / Freeman, J. / Chang, S. / Sauder, J.M. / Burley, S.K. / Almo, S.C.
History
DepositionJul 13, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 21, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.2Nov 21, 2018Group: Data collection / Structure summary / Category: audit_author / Item: _audit_author.identifier_ORCID
Revision 1.3Feb 10, 2021Group: Database references / Derived calculations / Structure summary
Category: audit_author / citation_author ...audit_author / citation_author / struct_ref_seq_dif / struct_site
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID ..._audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Thio-disulfide isomerase/thioredoxin
B: Thio-disulfide isomerase/thioredoxin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,5324
Polymers34,4142
Non-polymers1182
Water6,017334
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2500 Å2
ΔGint-18 kcal/mol
Surface area13010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.237, 63.237, 152.535
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11A-224-

HOH

21A-263-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

-
Components

#1: Protein Thio-disulfide isomerase/thioredoxin


Mass: 17206.885 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Strain: HB27 / Gene: TT_C1822 / Plasmid: BC-PSGX3(BC) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-CODON+RIL(STRATAGENE)
Tissue fraction (production host): BL21(DE3)-CODON+RIL(STRATAGENE)
References: UniProt: Q72GM6
#2: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 334 / 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: 2.58 Å3/Da / Density % sol: 52.38 %
Crystal growpH: 4.6
Details: 0.1M SODIUM ACETATE PH 4.6, 30% PEG4000, 200MM AMMONIUM ACETATE, 10% GLYCEROL, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 294K

-
Data collection

DiffractionMean temperature: 90 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.9789
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 18, 2009 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9789 Å / Relative weight: 1
ReflectionResolution: 1.76→50 Å / Num. obs: 35917 / % possible obs: 100 % / Observed criterion σ(I): -5 / Redundancy: 9.6 % / Biso Wilson estimate: 21.982 Å2 / Rsym value: 0.071 / Net I/σ(I): 7
Reflection shellResolution: 1.76→1.82 Å / Redundancy: 9.4 % / Rmerge(I) obs: 0.46 / Mean I/σ(I) obs: 2.1 / % possible all: 100

-
Processing

Software
NameVersionClassification
SHELXDphasing
REFMAC5.3.0034refinement
DENZOdata reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 1.76→20 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.952 / SU B: 1.955 / SU ML: 0.063 / Cross valid method: THROUGHOUT / ESU R: 0.097 / ESU R Free: 0.101 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20398 1121 3.1 %RANDOM
Rwork0.16289 ---
obs0.16411 34745 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: 25.87 Å2
Baniso -1Baniso -2Baniso -3
1-0.95 Å20.48 Å20 Å2
2--0.95 Å20 Å2
3----1.43 Å2
Refinement stepCycle: LAST / Resolution: 1.76→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2235 0 8 334 2577
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0222426
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.7461.9863334
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg21.3745317
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.89121.731104
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.34615398
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.4521527
X-RAY DIFFRACTIONr_chiral_restr0.1580.2375
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.021883
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1830.31152
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3120.51625
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1940.5474
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1420.349
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2180.550
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.79721522
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it5.0432443
X-RAY DIFFRACTIONr_scbond_it6.18631010
X-RAY DIFFRACTIONr_scangle_it8.8365873
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 1033 / Refine-ID: X-RAY DIFFRACTION

TypeRms dev position (Å)Weight position
loose positional0.555
loose thermal3.4710
LS refinement shellResolution: 1.76→1.805 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.254 84 -
Rwork0.216 2502 -
obs--100 %

+
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