[English] 日本語
Yorodumi
- PDB-6lds: Structure of a K245A mutant of L-tyrosine decarboxylase from Meth... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6lds
TitleStructure of a K245A mutant of L-tyrosine decarboxylase from Methanocaldococcus jannaschii complexed with L-Tyr: External aldimine form
ComponentsL-tyrosine/L-aspartate decarboxylase
KeywordsLYASE / PLP dependent decarboxylase / Catalytic Domain / Models / Molecular / Protein Conformation / PLP / Tyrosine / External aldimine / Tyrosine Decarboxylase / Structure-Activity Relationship / Dunathan alignment
Function / homology
Function and homology information


methanofuran biosynthetic process / tyrosine decarboxylase / tyrosine decarboxylase activity / aspartate 1-decarboxylase / aspartate 1-decarboxylase activity / carboxylic acid metabolic process / coenzyme A biosynthetic process / pyridoxal phosphate binding
Similarity search - Function
Decarboxylase MfnA, archaea / : / Pyridoxal phosphate-dependent decarboxylase / Pyridoxal-dependent decarboxylase conserved domain / Pyridoxal phosphate-dependent transferase, small domain / Pyridoxal phosphate-dependent transferase, major domain / Pyridoxal phosphate-dependent transferase
Similarity search - Domain/homology
Chem-0PR / L-tyrosine/L-aspartate decarboxylase
Similarity search - Component
Biological speciesMethanocaldococcus jannaschii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsManoj, N. / Gayathri, S.C.
Citation
Journal: J.Struct.Biol. / Year: 2019
Title: Structural insights into the mechanism of internal aldimine formation and catalytic loop dynamics in an archaeal Group II decarboxylase.
Authors: Chellam Gayathri, S. / Manoj, N.
#1: Journal: J. Struct. Biol. / Year: 2019
Title: Structural insights into the mechanism of internal aldimine formation and catalytic loop dynamics in an archaeal Group II decarboxylase.
Authors: Gayathri, S.C. / Manoj, N.
History
DepositionNov 23, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 2, 2020Provider: repository / Type: Initial release
Revision 1.1Dec 16, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Nov 22, 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: L-tyrosine/L-aspartate decarboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,5748
Polymers47,6011
Non-polymers9737
Water4,612256
1
A: L-tyrosine/L-aspartate decarboxylase
hetero molecules

A: L-tyrosine/L-aspartate decarboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,14716
Polymers95,2012
Non-polymers1,94614
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area11160 Å2
ΔGint-93 kcal/mol
Surface area26920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)98.420, 98.420, 122.030
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212

-
Components

#1: Protein L-tyrosine/L-aspartate decarboxylase / TDC/ADC


Mass: 47600.730 Da / Num. of mol.: 1 / Mutation: K245A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440) (archaea)
Strain: ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440
Gene: mfnA, MJ0050 / Plasmid: pSpeedET / Details (production host): Bacterial expression vector / Production host: Escherichia coli B (bacteria) / Strain (production host): B
References: UniProt: Q60358, aspartate 1-decarboxylase, tyrosine decarboxylase
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-0PR / N-({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methyl)-L-tyrosine / PHOSPHO-5'-PYRIDOXYL TYROSINE


Type: L-peptide linking / Mass: 412.331 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H21N2O8P / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 256 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Nonpolymer detailsAuthors state that the ligand in this entry has a protonated N1 atom and the corresponding hydrogen ...Authors state that the ligand in this entry has a protonated N1 atom and the corresponding hydrogen atom is labelled as H1. This is a different form of 0PR.

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.1 Å3/Da / Density % sol: 60.37 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.4
Details: 0.1M sodium citrate pH 5.4, 0.2M sodium potassium tartarate, 2.0M ammonium sulphate

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.979 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Oct 4, 2015
RadiationMonochromator: SI (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.77→51.86 Å / Num. obs: 58830 / % possible obs: 100 % / Redundancy: 8.1 % / Biso Wilson estimate: 24.8 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.078 / Rpim(I) all: 0.028 / Rrim(I) all: 0.083 / Net I/σ(I): 16.1
Reflection shellResolution: 1.77→1.81 Å / Redundancy: 6.9 % / Rmerge(I) obs: 1.179 / Mean I/σ(I) obs: 1.6 / Num. unique obs: 3301 / CC1/2: 0.824 / Rpim(I) all: 0.465 / Rrim(I) all: 1.272 / % possible all: 100

-
Processing

Software
NameVersionClassification
PHENIX1.17_3644refinement
Aimless0.5.17data scaling
PDB_EXTRACT3.25data extraction
iMOSFLMv7.1data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6LDR

6ldr


Resolution: 1.8→49.21 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 17.93
RfactorNum. reflection% reflectionSelection details
Rfree0.1955 2770 5 %Random
Rwork0.1673 ---
obs0.1687 56075 100 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 90.35 Å2 / Biso mean: 29.914 Å2 / Biso min: 12.73 Å2
Refinement stepCycle: final / Resolution: 1.8→49.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2935 0 93 256 3284
Biso mean--38.75 36.19 -
Num. residues----382
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0683092
X-RAY DIFFRACTIONf_angle_d0.9724183
X-RAY DIFFRACTIONf_dihedral_angle_d12.9351854
X-RAY DIFFRACTIONf_chiral_restr0.063470
X-RAY DIFFRACTIONf_plane_restr0.007543
LS refinement shellResolution: 1.8→1.83 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.2584 137 -
Rwork0.2404 2624 -
obs--100 %

+
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