[English] 日本語
Yorodumi
- PDB-3v15: Crystal structure of the Fe(II)/alpha-ketoglutarate dependent tau... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3v15
TitleCrystal structure of the Fe(II)/alpha-ketoglutarate dependent taurine dioxygenase from Pseudomonas putida KT2440
ComponentsAlpha-ketoglutarate-dependent taurine dioxygenase
KeywordsOXIDOREDUCTASE / jelly roll motif / dioxygenase / alpha-ketoglutarate / Fe(II)
Function / homology
Function and homology information


sulfonate dioxygenase activity / sulfur compound catabolic process / taurine dioxygenase / taurine dioxygenase activity / iron ion binding / identical protein binding / cytoplasm
Similarity search - Function
CHASE domain / Clavaminate synthase-like / Double-stranded beta-helix / TauD/TfdA-like domain / Taurine catabolism dioxygenase TauD, TfdA family / Taurine dioxygenase TauD-like superfamily / 4-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Alpha-ketoglutarate-dependent taurine dioxygenase
Similarity search - Component
Biological speciesPseudomonas putida (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsKnauer, S.H. / Dobbek, H.
CitationJournal: Febs J. / Year: 2012
Title: The Fe(II) / alpha-ketoglutarate dependent taurine dioxygenases from Pseudomonas putida and Escherichia coli are tetramers
Authors: Knauer, S.H. / Hartl-Spiegelhauer, O. / Schwarzinger, S. / Hanzelmann, P. / Dobbek, H.
History
DepositionDec 9, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 18, 2012Provider: repository / Type: Initial release
Revision 1.1Jun 26, 2013Group: Database references
Revision 1.2Sep 13, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Alpha-ketoglutarate-dependent taurine dioxygenase
C: Alpha-ketoglutarate-dependent taurine dioxygenase
B: Alpha-ketoglutarate-dependent taurine dioxygenase
D: Alpha-ketoglutarate-dependent taurine dioxygenase


Theoretical massNumber of molelcules
Total (without water)124,5364
Polymers124,5364
Non-polymers00
Water5,116284
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6840 Å2
ΔGint-34 kcal/mol
Surface area45310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.889, 101.850, 162.771
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein
Alpha-ketoglutarate-dependent taurine dioxygenase


Mass: 31134.020 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas putida (bacteria) / Strain: KT 2440 / Gene: PP0230, PP_0230, tauD / Plasmid: pET11a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q88RA3, taurine dioxygenase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 284 / 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: 2.83 Å3/Da / Density % sol: 56.46 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: reservoir solution: 20 % (w/v) PEG 5,000 MME, 0.1 M Bis Tris/HCl (pH 6.5) protein solution: 21 mg/ml protein in 25 mM Tris/HCl (pH 7.7) containing 10 mM taurine, 0.1 (NH4)2SO4 and 20 % (v/v) ...Details: reservoir solution: 20 % (w/v) PEG 5,000 MME, 0.1 M Bis Tris/HCl (pH 6.5) protein solution: 21 mg/ml protein in 25 mM Tris/HCl (pH 7.7) containing 10 mM taurine, 0.1 (NH4)2SO4 and 20 % (v/v) glycerol, VAPOR DIFFUSION, SITTING DROP, temperature 289K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: OTHER / Wavelength: 1.5418 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Nov 20, 2006
RadiationMonochromator: osmic mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.6→30 Å / Num. all: 44171 / Num. obs: 44029 / % possible obs: 99.7 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 4.6 % / Rsym value: 0.088 / Net I/σ(I): 18.4
Reflection shellResolution: 2.6→2.7 Å / Redundancy: 4.6 % / Num. unique all: 4669 / Rsym value: 0.595 / % possible all: 99.7

-
Processing

Software
NameVersionClassification
MAR345dtbdata collection
AMoREphasing
PHENIX(phenix.refine: 1.6.1_357)refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3PVJ

3pvj


Resolution: 2.6→28.78 Å / SU ML: 0.38 / σ(F): 1.99 / Phase error: 23.85 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2544 2201 5 %random
Rwork0.1829 ---
obs0.1864 44004 99.72 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 51.583 Å2 / ksol: 0.346 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-15.8789 Å2-0 Å2-0 Å2
2---6.0157 Å20 Å2
3----9.8632 Å2
Refinement stepCycle: LAST / Resolution: 2.6→28.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8764 0 0 284 9048
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0089004
X-RAY DIFFRACTIONf_angle_d1.15812320
X-RAY DIFFRACTIONf_dihedral_angle_d14.9763268
X-RAY DIFFRACTIONf_chiral_restr0.0731378
X-RAY DIFFRACTIONf_plane_restr0.0061638
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6-2.69290.31052170.21244125X-RAY DIFFRACTION100
2.6929-2.80060.27312170.20874110X-RAY DIFFRACTION100
2.8006-2.92790.28662170.20774129X-RAY DIFFRACTION100
2.9279-3.08210.28512190.20744156X-RAY DIFFRACTION100
3.0821-3.2750.2812190.19364158X-RAY DIFFRACTION100
3.275-3.52740.27012180.18374148X-RAY DIFFRACTION100
3.5274-3.88170.24762210.17694205X-RAY DIFFRACTION100
3.8817-4.44160.20052210.14454188X-RAY DIFFRACTION100
4.4416-5.58920.23922220.14814232X-RAY DIFFRACTION100
5.5892-28.78190.21432300.17324352X-RAY DIFFRACTION99
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)
11.2506-0.54880.37350.4987-0.17180.73310.15240.4742-0.0555-0.182-0.198-0.08060.23430.4729-0.00430.0780.07540.05020.4573-0.08260.26554.92414.6092-25.2766
20.22640.03790.33890.3735-0.52821.39980.0128-0.07540.03770.05420.08040.0711-0.0581-0.3127-0.06980.00890.03780.03790.2188-0.00890.1644-25.292416.7435-22.203
30.21370.2815-0.0851.236-0.75461.26810.09210.02180.08820.3352-0.00520.2166-0.3006-0.1292-0.06630.0032-0.02730.0820.1301-0.06810.2059-14.64639.924322.2548
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A
2X-RAY DIFFRACTION2chain B
3X-RAY DIFFRACTION3chain C

+
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