[English] 日本語
Yorodumi
- PDB-2ypm: Crystal Structure of Ancestral Thioredoxin Relative to Last Anima... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2ypm
TitleCrystal Structure of Ancestral Thioredoxin Relative to Last Animal and Fungi Common Ancestor (LAFCA) from the Precambrian Period
ComponentsLAFCA THIOREDOXIN
KeywordsOXIDOREDUCTASE / ANCESTRAL RECONSTRUCTED
Function / homologyGlutaredoxin / Glutaredoxin / 3-Layer(aba) Sandwich / Alpha Beta
Function and homology information
Biological speciesSYNTHETIC CONSTRUCT (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.199 Å
AuthorsGavira, J.A. / Ingles-Prieto, A. / Ibarra-Molero, B. / Sanchez-Ruiz, J.M.
CitationJournal: Structure / Year: 2013
Title: Conservation of Protein Structure Over Four Billion Years
Authors: Ingles-Prieto, A. / Ibarra-Molero, B. / Delgado-Delgado, A. / Perez-Jimenez, R. / Fernandez, J.M. / Gaucher, E.A. / Sanchez-Ruiz, J.M. / Gavira, J.A.
History
DepositionOct 30, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 21, 2013Provider: repository / Type: Initial release
Revision 1.1Sep 25, 2013Group: Database references
Revision 1.2Mar 6, 2019Group: Advisory / Data collection ...Advisory / Data collection / Experimental preparation / Other
Category: database_PDB_rev / database_PDB_rev_record ...database_PDB_rev / database_PDB_rev_record / exptl_crystal_grow / pdbx_database_proc / pdbx_database_status / pdbx_unobs_or_zero_occ_atoms / struct_biol
Item: _exptl_crystal_grow.method / _exptl_crystal_grow.temp / _pdbx_database_status.recvd_author_approval
Revision 1.3Dec 20, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: LAFCA THIOREDOXIN


Theoretical massNumber of molelcules
Total (without water)11,9071
Polymers11,9071
Non-polymers00
Water93752
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)37.493, 42.791, 55.920
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein LAFCA THIOREDOXIN


Mass: 11906.608 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SYNTHETIC CONSTRUCT (others) / Plasmid: PET30A PLUS / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: thioredoxin-disulfide reductase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 52 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsANCESTRAL RECONSTRUCTED

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 1.95 Å3/Da / Density % sol: 36.82 % / Description: NONE
Crystal growTemperature: 277 K / Method: counter-diffusion / pH: 5.5
Details: COUNTER-DIFFUSION: 0.1M TRIS-HCL, 30% PEG 4000, 0.2 M MGCL2, PH 8.50, T 277 K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM16 / Wavelength: 0.98
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Nov 20, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.2→20 Å / Num. obs: 4904 / % possible obs: 100 % / Observed criterion σ(I): 1 / Redundancy: 10.4 % / Biso Wilson estimate: 29.19 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 23.26
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 10.7 % / Rmerge(I) obs: 0.49 / Mean I/σ(I) obs: 4.95 / % possible all: 100

-
Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1ERV

1erv


Resolution: 2.199→19.983 Å / SU ML: 0.26 / σ(F): 1.35 / Phase error: 23.7 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2387 227 4.7 %
Rwork0.1666 --
obs0.1701 4874 99.59 %
Solvent computationShrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 50.384 Å2 / ksol: 0.375 e/Å3
Displacement parametersBiso mean: 31 Å2
Baniso -1Baniso -2Baniso -3
1--1.5204 Å20 Å20 Å2
2---1.2767 Å20 Å2
3---2.7972 Å2
Refinement stepCycle: LAST / Resolution: 2.199→19.983 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms810 0 0 52 862
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.008888
X-RAY DIFFRACTIONf_angle_d1.0871204
X-RAY DIFFRACTIONf_dihedral_angle_d15.476343
X-RAY DIFFRACTIONf_chiral_restr0.075136
X-RAY DIFFRACTIONf_plane_restr0.005156
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1985-2.76870.30691090.1942253X-RAY DIFFRACTION99
2.7687-19.98360.2141180.15652394X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
15.66530.6083-0.7412.2074-0.02333.3390.26770.56720.0979-0.7711-0.1180.43470.1099-0.31140.18820.24580.0887-0.12490.1189-0.03710.194-22.74383.63814.2795
23.9217-0.35550.25853.1358-0.12963.0976-0.0276-0.00020.1110.06520.2342-0.3422-0.35120.36380.01260.1389-0.0320.03930.0952-0.07890.1047-12.8836-1.065511.2743
31.6762-0.429-2.05530.96791.37113.3513-0.08830.4977-0.1872-0.2107-0.12120.57-0.0102-0.77810.06930.1296-0.0509-0.08960.36710.0670.4586-29.0725-4.192111.2887
42.6110.93370.1271.29730.34441.1981-0.01020.17490.0159-0.18080.19390.2640.0863-0.0986-0.00920.1262-0.16880.05490.1222-0.0210.173-19.4881-8.10235.2875
50.35250.34780.47290.7886-1.25427.3101-0.21920.2319-0.2375-0.23990.0084-0.28270.50740.02140.00550.1406-0.06890.10280.1314-0.05770.2011-13.948-11.28775.2607
62.26210.247-2.01012.98850.05794.8619-0.1103-0.0505-0.1245-0.18950.2461-0.675-0.11390.4501-0.1330.1279-0.04620.09290.1422-0.09380.3324-5.1826-8.44927.2397
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND (RESSEQ 1:17)
2X-RAY DIFFRACTION2CHAIN A AND (RESSEQ 18:58)
3X-RAY DIFFRACTION3CHAIN A AND (RESSEQ 59:66)
4X-RAY DIFFRACTION4CHAIN A AND (RESSEQ 67:83)
5X-RAY DIFFRACTION5CHAIN A AND (RESSEQ 84:93)
6X-RAY DIFFRACTION6CHAIN A AND (RESSEQ 94:105)

+
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