[English] 日本語
Yorodumi
- PDB-4xhm: Archaeoglobus fulgidus thioredoxin 3 M60H -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4xhm
TitleArchaeoglobus fulgidus thioredoxin 3 M60H
ComponentsThioredoxin (Trx-3)
KeywordsOXIDOREDUCTASE / disulfide / thioredoxin
Function / homology
Function and homology information


glycerol ether metabolic process / protein-disulfide reductase activity / cell redox homeostasis
Similarity search - Function
Thioredoxin / Thioredoxin / Thioredoxin domain profile. / Thioredoxin domain / Glutaredoxin / Glutaredoxin / Thioredoxin-like superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesArchaeoglobus fulgidus (archaea)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.95 Å
AuthorsDey, M. / Bjork, R.E. / Drennan, C.L.
Funding support United States, 2items
OrganizationGrant numberCountry
Howard Hughes Medical Institute (HHMI) United States
National Science Foundation (NSF, United States)MCB 1122977 United States
CitationJournal: Plos One
Title: Rheostat Re-Wired: Alternative Hypotheses for the Control of Thioredoxin Reduction Potentials.
Authors: Bewley, K.D. / Dey, M. / Bjork, R.E. / Mitra, S. / Chobot, S.E. / Drennan, C.L. / Elliott, S.J.
History
DepositionJan 5, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 29, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 6, 2017Group: Advisory / Author supporting evidence ...Advisory / Author supporting evidence / Derived calculations / Source and taxonomy
Category: entity_src_gen / pdbx_audit_support ...entity_src_gen / pdbx_audit_support / pdbx_struct_assembly / pdbx_struct_oper_list / pdbx_validate_close_contact
Item: _entity_src_gen.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization ..._entity_src_gen.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Nov 20, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Thioredoxin (Trx-3)
B: Thioredoxin (Trx-3)


Theoretical massNumber of molelcules
Total (without water)31,3172
Polymers31,3172
Non-polymers00
Water5,134285
1
A: Thioredoxin (Trx-3)


Theoretical massNumber of molelcules
Total (without water)15,6581
Polymers15,6581
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Thioredoxin (Trx-3)


Theoretical massNumber of molelcules
Total (without water)15,6581
Polymers15,6581
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)49.564, 56.905, 100.076
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein Thioredoxin (Trx-3)


Mass: 15658.253 Da / Num. of mol.: 2 / Mutation: M60H
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Archaeoglobus fulgidus (strain ATCC 49558 / VC-16 / DSM 4304 / JCM 9628 / NBRC 100126) (archaea)
Strain: ATCC 49558 / VC-16 / DSM 4304 / JCM 9628 / NBRC 100126
Gene: AF_1284 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta (DE3)pLysS / References: UniProt: O28984
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 285 / 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: 2.25 Å3/Da / Density % sol: 45.11 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 1.0 ul of 20 mg/ml protein solution (in 10 mM HEPES pH 7.0 and 20 mM NaCl) and 1.0 ul of precipitant solution containing 60% Tacsimate, pH 7.0 using sitting drop method. Rod-shaped crystals ...Details: 1.0 ul of 20 mg/ml protein solution (in 10 mM HEPES pH 7.0 and 20 mM NaCl) and 1.0 ul of precipitant solution containing 60% Tacsimate, pH 7.0 using sitting drop method. Rod-shaped crystals of approximately 100-150 um grew in 3-4 days. Crystals were cryo-protected in precipitant solution containing 10% glycerol by soaking for 2-5 minutes before flash-freezing in liquid nitrogen

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.541 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Apr 15, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.541 Å / Relative weight: 1
ReflectionResolution: 1.95→50 Å / Num. obs: 18906 / % possible obs: 88.4 % / Redundancy: 3.9 % / Biso Wilson estimate: 22.03 Å2 / Rsym value: 0.052 / Χ2: 0.968 / Net I/σ(I): 25.422 / Num. measured all: 74266
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. unique allΧ2% possible all
1.95-2.020.2325.2520850.86499.7
2.02-2.10.24112680.85760.2
2.1-2.20.13120960.777100
2.2-2.310.12112870.87161.2
2.31-2.460.08421210.802100
2.46-2.650.07721120.919100
2.65-2.910.07221401.31299.8
2.91-3.330.0421361.025100
3.33-4.20.03613741.3263
4.2-500.0252287199.2

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
Cootmodel building
PHENIXrefinement
CNSrefinement
REFMACrefinement
PDB_EXTRACT3.15data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 207K

207k


Resolution: 1.95→24.887 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / Phase error: 22.88 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2499 969 5.17 %random
Rwork0.1906 17790 --
obs0.1936 18759 88.11 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 78.75 Å2 / Biso mean: 26.5884 Å2 / Biso min: 11.72 Å2
Refinement stepCycle: final / Resolution: 1.95→24.887 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1739 0 0 285 2024
Biso mean---32.39 -
Num. residues----219
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0031826
X-RAY DIFFRACTIONf_angle_d0.7492487
X-RAY DIFFRACTIONf_chiral_restr0.028278
X-RAY DIFFRACTIONf_plane_restr0.004320
X-RAY DIFFRACTIONf_dihedral_angle_d9.882697
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.95-2.05280.25171650.21282709X-RAY DIFFRACTION96.5
2.0528-2.18130.24711090.20282111X-RAY DIFFRACTION74.1
2.1813-2.34960.25111150.19412066X-RAY DIFFRACTION72.7
2.3496-2.58580.24821610.18212848X-RAY DIFFRACTION100
2.5858-2.95950.29011440.23382857X-RAY DIFFRACTION99.4
2.9595-3.72660.2831320.18932634X-RAY DIFFRACTION90.1
3.7266-24.88940.19761430.15862565X-RAY DIFFRACTION84.5

+
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://pdbjlvh1.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