[English] 日本語
Yorodumi
- PDB-3h79: Crystal structure of Trypanosoma cruzi thioredoxin-like hypotheti... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3h79
TitleCrystal structure of Trypanosoma cruzi thioredoxin-like hypothetical protein Q4DV70
ComponentsThioredoxin-like protein
KeywordsUNKNOWN FUNCTION / thioredoxin fold / catalytic cysteines missing
Function / homology
Function and homology information


protein disulfide isomerase activity / protein folding / endoplasmic reticulum
Similarity search - Function
: / Thioredoxin / Thioredoxin domain / Glutaredoxin / Glutaredoxin / Thioredoxin-like superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
THIOCYANATE ION / Thioredoxin domain-containing protein
Similarity search - Component
Biological speciesTrypanosoma cruzi (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsSantos, C.R. / Fessel, M.R. / Vieira, L.C. / Krieger, M.A. / Goldenberg, S. / Guimaraes, B.G. / Zanchin, N.I.T. / Barbosa, J.A.R.G.
CitationJournal: TO BE PUBLISHED
Title: Crystal structure of Trypanosoma cruzi thioredoxin-like hypothetical protein Q4DV70
Authors: Santos, C.R. / Fessel, M.R. / Vieira, L.C. / Krieger, M.A. / Goldenberg, S. / Guimaraes, B.G. / Zanchin, N.I.T. / Barbosa, J.A.R.G.
History
DepositionApr 24, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 12, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Refinement description / Version format compliance
Revision 1.2Nov 1, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software / Item: _software.name
Revision 1.3Sep 6, 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_unobs_or_zero_occ_atoms / 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 / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 999author states that the sequence conflict at residue 94 is likely due to the strain variation

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Thioredoxin-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,9442
Polymers14,8861
Non-polymers581
Water2,090116
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)35.042, 50.321, 61.179
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein Thioredoxin-like protein


Mass: 14885.673 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trypanosoma cruzi (eukaryote) / Strain: Dm28c
Gene: Tc00.1047053508173.160, Trypanosoma cruzi strain CL Brener hypothetical protein partial mRNA
Plasmid: pET-TEV / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)slyD- / References: UniProt: Q4DV70
#2: Chemical ChemComp-SCN / THIOCYANATE ION


Mass: 58.082 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CNS
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 116 / 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: 1.81 Å3/Da / Density % sol: 32.11 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.9
Details: 25% PEG 1500, 0.2M sodium thiocyanate, 0.01M phenol, 10% ethyleneglycol, pH 6.9, VAPOR DIFFUSION, HANGING DROP, temperature 291K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: LNLS / Beamline: W01B-MX2 / Wavelength: 1.459 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jan 21, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.459 Å / Relative weight: 1
ReflectionResolution: 1.5→20 Å / Num. all: 17813 / Num. obs: 17813 / % possible obs: 99.1 % / Redundancy: 4.7 % / Biso Wilson estimate: 16.9 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 23.9
Reflection shellResolution: 1.5→1.55 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.24 / Mean I/σ(I) obs: 4.7 / Num. unique all: 1619 / % possible all: 95.9

-
Processing

Software
NameVersionClassification
MAR345data collection
MOLREPphasing
REFMAC5.5.0066refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2B5E

2b5e


Resolution: 1.5→19.43 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.941 / SU B: 2.875 / SU ML: 0.049 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.082 / ESU R Free: 0.088 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22361 880 5 %RANDOM
Rwork0.18 ---
obs0.18209 16892 99.17 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 12.591 Å2
Baniso -1Baniso -2Baniso -3
1--0.71 Å20 Å20 Å2
2--0.63 Å20 Å2
3---0.08 Å2
Refinement stepCycle: LAST / Resolution: 1.5→19.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms965 0 3 116 1084
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0260.0221020
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.1581.9491375
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1335114
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.87722.41458
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.3915185
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.2221513
X-RAY DIFFRACTIONr_chiral_restr0.1680.2141
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.021794
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.4241.5580
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.2132954
X-RAY DIFFRACTIONr_scbond_it3.3013440
X-RAY DIFFRACTIONr_scangle_it5.0254.5421
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.5→1.539 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.376 65 -
Rwork0.316 1159 -
obs--94.74 %
Refinement TLS params.Method: refined / Origin x: 9.9112 Å / Origin y: 0.8025 Å / Origin z: -9.6849 Å
111213212223313233
T0.0195 Å2-0.0019 Å20.0065 Å2-0.0197 Å2-0.0017 Å2--0.004 Å2
L1.742 °2-0.4256 °2-0.0698 °2-1.2164 °20.1979 °2--0.6072 °2
S-0.0095 Å °-0.0199 Å °-0.0009 Å °0.0366 Å °-0.0174 Å °-0.0044 Å °0.0114 Å °0.031 Å °0.0269 Å °

+
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