[English] 日本語
Yorodumi
- PDB-5hr3: Crystal structure of thioredoxin N106A mutant -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5hr3
TitleCrystal structure of thioredoxin N106A mutant
ComponentsThioredoxin
KeywordsOXIDOREDUCTASE / thioredoxin / thiol redox-reactions
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 / ETHANOL / Thioredoxin / Thioredoxin 1
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.101 Å
AuthorsNoguera, M.E. / Vazquez, D.S. / Howard, E.I. / Cousido-Siah, A. / Mitschler, A. / Podjarny, A. / Santos, J.
CitationJournal: Sci Rep / Year: 2017
Title: Structural variability of E. coli thioredoxin captured in the crystal structures of single-point mutants.
Authors: Noguera, M.E. / Vazquez, D.S. / Ferrer-Sueta, G. / Agudelo, W.A. / Howard, E. / Rasia, R.M. / Manta, B. / Cousido-Siah, A. / Mitschler, A. / Podjarny, A. / Santos, J.
History
DepositionJan 22, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 22, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 27, 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 / pdbx_struct_conn_angle / struct_conn / struct_ncs_dom_lim
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_asym_id / _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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_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.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_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_asym_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_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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Thioredoxin
B: Thioredoxin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,9308
Polymers23,5512
Non-polymers3796
Water3,369187
1
A: Thioredoxin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,9494
Polymers11,7761
Non-polymers1733
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Thioredoxin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,9814
Polymers11,7761
Non-polymers2063
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)29.238, 33.124, 47.185
Angle α, β, γ (deg.)75.750, 88.850, 68.830
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resseq 2:57 or resseq 59:72 or resseq 74:103 or resseq 105:108))
21(chain B and (resseq 2:57 or resseq 59:72 or resseq 74:103 or resseq 105:108))

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ASPASPLYSLYS(chain A and (resseq 2:57 or resseq 59:72 or resseq 74:103 or resseq 105:108))AA2 - 573 - 58
12ASNASNILEILE(chain A and (resseq 2:57 or resseq 59:72 or resseq 74:103 or resseq 105:108))AA59 - 7260 - 73
13GLYGLYLEULEU(chain A and (resseq 2:57 or resseq 59:72 or resseq 74:103 or resseq 105:108))AA74 - 10375 - 104
14ALAALAALAALA(chain A and (resseq 2:57 or resseq 59:72 or resseq 74:103 or resseq 105:108))AA105 - 108106 - 109
21ASPASPLYSLYS(chain B and (resseq 2:57 or resseq 59:72 or resseq 74:103 or resseq 105:108))BB2 - 573 - 58
22ASNASNILEILE(chain B and (resseq 2:57 or resseq 59:72 or resseq 74:103 or resseq 105:108))BB59 - 7260 - 73
23GLYGLYLEULEU(chain B and (resseq 2:57 or resseq 59:72 or resseq 74:103 or resseq 105:108))BB74 - 10375 - 104
24ALAALAALAALA(chain B and (resseq 2:57 or resseq 59:72 or resseq 74:103 or resseq 105:108))BB105 - 108106 - 109

-
Components

#1: Protein Thioredoxin


Mass: 11775.557 Da / Num. of mol.: 2 / Mutation: N106A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: trxA, BN17_37301, ECs4714 / Production host: Escherichia coli (E. coli) / References: UniProt: C3SKR2, UniProt: P0AA25*PLUS
#2: Chemical ChemComp-CU / COPPER (II) ION


Mass: 63.546 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cu
#3: Chemical ChemComp-EOH / ETHANOL


Mass: 46.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 187 / 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: 1.75 Å3/Da / Density % sol: 29.66 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop
Details: The drop was a 1:1 mix of protein (10 mg/ml, in water) and reservoir solution (100 mM sodium acetate, 4 mM CuSO4, 25 % ethanol, pH 4.25)

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 0.9202 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Mar 14, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9202 Å / Relative weight: 1
ReflectionResolution: 1.1→16.227 Å / Num. obs: 59930 / % possible obs: 93 % / Redundancy: 2 % / Biso Wilson estimate: 10.06 Å2 / Rmerge(I) obs: 0.036 / Χ2: 1.067 / Net I/σ(I): 14.8 / Num. measured all: 117251
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
1.1-1.141.90.24257571.08389.2
1.14-1.181.90.18658321.07591
1.18-1.2420.15859201.07591.9
1.24-1.320.13559921.0792.9
1.3-1.3920.10660161.0693
1.39-1.4920.08360761.07194.6
1.49-1.6420.06161311.04394.7
1.64-1.8820.04661611.04695.6
1.88-2.3720.0362121.08596.1
2.37-501.90.02258331.06590.6

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassification
HKL-2000data scaling
PHASERphasing
PHENIXdev_2247refinement
PDB_EXTRACT3.15data extraction
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1KEB

1keb


Resolution: 1.101→16.227 Å / SU ML: 0.08 / Cross valid method: FREE R-VALUE / σ(F): 2 / Phase error: 15.63 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1634 3032 5.06 %Random selection
Rwork0.1419 56885 --
obs0.143 59917 92.69 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 89.86 Å2 / Biso mean: 17.0237 Å2 / Biso min: 6.35 Å2
Refinement stepCycle: final / Resolution: 1.101→16.227 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1626 0 26 187 1839
Biso mean--25.28 24.69 -
Num. residues----214
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0111687
X-RAY DIFFRACTIONf_angle_d1.2032293
X-RAY DIFFRACTIONf_chiral_restr0.09266
X-RAY DIFFRACTIONf_plane_restr0.008293
X-RAY DIFFRACTIONf_dihedral_angle_d14.822623
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A1189X-RAY DIFFRACTION6.144TORSIONAL
12B1189X-RAY DIFFRACTION6.144TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 22

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.101-1.1180.20161300.1912271240182
1.118-1.13630.20311260.18492505263190
1.1363-1.15590.1891250.16442509263491
1.1559-1.17690.17871170.15912605272291
1.1769-1.19950.19451400.15082535267592
1.1995-1.2240.17931340.1482625275992
1.224-1.25060.17061350.14812519265492
1.2506-1.27970.17821350.14162594272992
1.2797-1.31170.19121330.14082615274893
1.3117-1.34710.16081330.12862605273893
1.3471-1.38680.17161340.13132596273093
1.3868-1.43150.14711530.12812636278995
1.4315-1.48260.15831490.12512630277994
1.4826-1.54190.15011130.12692650276394
1.5419-1.61210.14841480.12542636278495
1.6121-1.6970.15211470.13032659280696
1.697-1.80320.17541700.13522638280896
1.8032-1.94220.14531370.13532676281395
1.9422-2.13720.17581430.13332654279796
2.1372-2.44560.15641600.13182699285997
2.4456-3.07770.16191520.14812708286098
3.0777-16.22840.15671180.15682320243883

+
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