[English] 日本語
Yorodumi
- PDB-6g3d: Crystal structure of Native EDDS lyase -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6g3d
TitleCrystal structure of Native EDDS lyase
ComponentsArgininosuccinate lyase
KeywordsLYASE / C-N Lyase / metal chelator / EDDS / tetramer / aspartase fumarase superfamily
Function / homology
Function and homology information


argininosuccinate lyase / argininosuccinate lyase activity / L-arginine biosynthetic process via ornithine / L-arginine biosynthetic process / cytosol
Similarity search - Function
Argininosuccinate lyase / Argininosuccinate lyase, C-terminal / Argininosuccinate lyase C-terminal / Fumarase/aspartase (C-terminal domain) / Fumarate lyase family / Fumarate lyase, N-terminal / Lyase / Ribonucleotide Reductase Protein R1; domain 1 / Fumarase/histidase, N-terminal / L-Aspartase-like ...Argininosuccinate lyase / Argininosuccinate lyase, C-terminal / Argininosuccinate lyase C-terminal / Fumarase/aspartase (C-terminal domain) / Fumarate lyase family / Fumarate lyase, N-terminal / Lyase / Ribonucleotide Reductase Protein R1; domain 1 / Fumarase/histidase, N-terminal / L-Aspartase-like / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Argininosuccinate lyase
Similarity search - Component
Biological speciesChelativorans sp.
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.221 Å
AuthorsPoddar, H. / Thunnissem, A.M.W.H. / Poelarends, G.J.
Funding support Netherlands, 1items
OrganizationGrant numberCountry
European Research Council242293 Netherlands
CitationJournal: Biochemistry / Year: 2018
Title: Structural Basis for the Catalytic Mechanism of Ethylenediamine- N, N'-disuccinic Acid Lyase, a Carbon-Nitrogen Bond-Forming Enzyme with a Broad Substrate Scope.
Authors: Poddar, H. / de Villiers, J. / Zhang, J. / Puthan Veetil, V. / Raj, H. / Thunnissen, A.W.H. / Poelarends, G.J.
History
DepositionMar 25, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 16, 2018Provider: repository / Type: Initial release
Revision 1.1May 23, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI ..._citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2May 30, 2018Group: Data collection / Database references / Category: citation / Item: _citation.title
Revision 1.3Jul 11, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.4Jan 17, 2024Group: 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: Argininosuccinate lyase


Theoretical massNumber of molelcules
Total (without water)55,7581
Polymers55,7581
Non-polymers00
Water4,702261
1
A: Argininosuccinate lyase

A: Argininosuccinate lyase

A: Argininosuccinate lyase

A: Argininosuccinate lyase


Theoretical massNumber of molelcules
Total (without water)223,0334
Polymers223,0334
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-x,-y+1,z1
crystal symmetry operation3_555-x,y,-z1
crystal symmetry operation4_565x,-y+1,-z1
Buried area31790 Å2
ΔGint-122 kcal/mol
Surface area59700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)144.395, 144.763, 147.618
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number22
Space group name H-MF222
Components on special symmetry positions
IDModelComponents
11A-829-

HOH

-
Components

#1: Protein Argininosuccinate lyase


Mass: 55758.246 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chelativorans sp. (strain BNC1) (bacteria)
Strain: BNC1 / Gene: Meso_0564 / Plasmid: pBADN / Production host: Escherichia coli (E. coli) / References: UniProt: Q11KV9
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 261 / 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: 3.46 Å3/Da / Density % sol: 64.44 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 0.1 M HEPES pH 7.5 and 4 M NaCl

-
Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.54 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Feb 11, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.22→51.7 Å / Num. obs: 37577 / % possible obs: 98.5 % / Redundancy: 4.1 % / Rmerge(I) obs: 0.151 / Net I/σ(I): 9.9
Reflection shellResolution: 2.22→2.27 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.544 / Mean I/σ(I) obs: 2.8 / % possible all: 94.4

-
Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1TJU,2E9F,1U15

1tju

2e9f

1u15


Resolution: 2.221→51.679 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 20.86
RfactorNum. reflection% reflection
Rfree0.224 1903 5.06 %
Rwork0.1824 --
obs0.1845 37577 98.55 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.221→51.679 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3805 0 0 261 4066
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0033876
X-RAY DIFFRACTIONf_angle_d0.5295260
X-RAY DIFFRACTIONf_dihedral_angle_d14.8492356
X-RAY DIFFRACTIONf_chiral_restr0.038611
X-RAY DIFFRACTIONf_plane_restr0.004684
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2214-2.27690.29511200.26532308X-RAY DIFFRACTION90
2.2769-2.33850.2491470.2262486X-RAY DIFFRACTION98
2.3385-2.40730.25571370.21512533X-RAY DIFFRACTION98
2.4073-2.4850.22841210.21882519X-RAY DIFFRACTION99
2.485-2.57380.26381350.21742548X-RAY DIFFRACTION99
2.5738-2.67690.27091490.20932511X-RAY DIFFRACTION99
2.6769-2.79870.32831470.22312549X-RAY DIFFRACTION99
2.7987-2.94620.2551220.22142589X-RAY DIFFRACTION99
2.9462-3.13080.28431480.20542546X-RAY DIFFRACTION100
3.1308-3.37250.21411450.19332551X-RAY DIFFRACTION100
3.3725-3.71180.19441270.15332607X-RAY DIFFRACTION100
3.7118-4.24870.16261390.13642603X-RAY DIFFRACTION100
4.2487-5.3520.16921340.13112621X-RAY DIFFRACTION100
5.352-51.69270.17431320.15332703X-RAY DIFFRACTION99

+
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