[English] 日本語
Yorodumi
- PDB-4hua: E. coli thioredoxin variant with (4R)-FluoroPro76 as single proli... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4hua
TitleE. coli thioredoxin variant with (4R)-FluoroPro76 as single proline residue
ComponentsThioredoxin-1
KeywordsOXIDOREDUCTASE / 4r-fluoroproline / cisproline / thioredoxin fold / protein disulfide oxidoreductase activity
Function / homology
Function and homology information


DNA polymerase processivity factor activity / protein-disulfide reductase activity / cell redox homeostasis / cytoplasm / cytosol
Similarity search - Function
Thioredoxin / Thioredoxin / Thioredoxin, conserved site / Thioredoxin family active site. / Thioredoxin domain profile. / Thioredoxin domain / Glutaredoxin / Glutaredoxin / Thioredoxin-like superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
COPPER (II) ION / Thioredoxin 1
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.1 Å
AuthorsScharer, M.A. / Rubini, M. / Capitani, G. / Glockshuber, R.
CitationJournal: Chembiochem / Year: 2013
Title: (4R)- and (4S)-Fluoroproline in the Conserved cis-Prolyl Peptide Bond of the Thioredoxin Fold: Tertiary Structure Context Dictates Ring Puckering.
Authors: Rubini, M. / Scharer, M.A. / Capitani, G. / Glockshuber, R.
History
DepositionNov 2, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 29, 2013Provider: repository / Type: Initial release
Revision 1.1Jul 3, 2013Group: Database references
Revision 1.2Oct 11, 2017Group: Advisory / Data collection / Refinement description
Category: pdbx_unobs_or_zero_occ_atoms / reflns_shell / software
Item: _reflns_shell.percent_possible_all / _software.name
Revision 1.3Sep 20, 2023Group: Advisory / Data collection ...Advisory / 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 / pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Dec 6, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.5Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Thioredoxin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,6652
Polymers11,6011
Non-polymers641
Water2,594144
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)88.360, 48.690, 31.490
Angle α, β, γ (deg.)90.000, 101.980, 90.000
Int Tables number5
Space group name H-MC121

-
Components

#1: Protein Thioredoxin-1


Mass: 11601.229 Da / Num. of mol.: 1 / Mutation: P34A, P40A, P64A, P68A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K-12 / Gene: trxA, fipA, tsnC / Plasmid: pTrx1P / Production host: Escherichia coli (E. coli) / Strain (production host): JM83 / References: UniProt: P0AA25
#2: Chemical ChemComp-CU / COPPER (II) ION


Mass: 63.546 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cu
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 144 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.86 Å3/Da / Density % sol: 56.93 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop / pH: 4.5
Details: 20 mM acetic acid-NaOH pH 4.5, 2 mM CuCl2, 35 % (v/v) MPD, VAPOR DIFFUSION, SITTING DROP, temperature 277.15K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorDetector: PIXEL / Date: Jun 18, 2012 / Details: mirrors
RadiationMonochromator: Bartels Monochromator with dual channel cut crystals
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionHighest resolution: 1 Å / Num. obs: 101582 / % possible obs: 73.1 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 12.007 Å2 / Rmerge(I) obs: 0.079 / Net I/σ(I): 11.45
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
1-1.10.9111.0216063474413.8
1.1-1.20.7011.7785801759773.3
1.2-1.40.513.041754712876596.7
1.4-1.60.2436.831121551663999.8
1.6-20.10814.741098521653699.7
2-40.04236.241029871513299.6
4-60.02562.1811058151999.9
6-80.02558.84283938499.5
8-100.0267.13962129100
10-200.01969.6283811898.3
20-300.02567.098815100
30-400.01860.5641100
400.02858.2113100

-
Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHENIX1.8_1069refinement
PDB_EXTRACT3.11data extraction
RemDAqdata collection
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4HU7

4hu7


Resolution: 1.1→43.217 Å / Occupancy max: 1 / Occupancy min: 0 / FOM work R set: 0.905 / SU ML: 0.1 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 17.04 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1719 2088 2.28 %random
Rwork0.1593 ---
obs0.1596 91593 87.77 %-
Solvent computationShrinkage radii: 1 Å / VDW probe radii: 1.3 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 43.17 Å2 / Biso mean: 12.3843 Å2 / Biso min: 2.85 Å2
Refinement stepCycle: LAST / Resolution: 1.1→43.217 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms815 0 1 144 960
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01944
X-RAY DIFFRACTIONf_angle_d1.0621282
X-RAY DIFFRACTIONf_chiral_restr0.067149
X-RAY DIFFRACTIONf_plane_restr0.003166
X-RAY DIFFRACTIONf_dihedral_angle_d12.593342
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 15

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.1-1.12560.3233750.30243255333047
1.1256-1.15380.3093990.27654152425162
1.1538-1.1850.26021170.24455167528476
1.185-1.21990.20671370.21285623576083
1.2199-1.25920.21791420.20265927606987
1.2592-1.30420.22761420.18815966610889
1.3042-1.35650.19471410.17896220636192
1.3565-1.41820.19471480.15956357650594
1.4182-1.4930.19121440.14486557670196
1.493-1.58650.14641560.1346622677898
1.5865-1.7090.1811520.13426646679898
1.709-1.8810.13051590.13546733689299
1.881-2.15320.18541580.13946722688099
2.1532-2.71270.16521600.15436760692099
2.7127-43.25050.14061580.152567986956100

+
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