[English] 日本語
Yorodumi
- PDB-9evv: His579Leu variant of L-arabinonate dehydratase co-crystallized wi... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9evv
TitleHis579Leu variant of L-arabinonate dehydratase co-crystallized with 2-oxobutyrate
ComponentsL-arabinonate dehydratase
KeywordsLYASE / arabinonate dehydratase / IlvD/EDD superfamily / dihydroxy acid dehydratase / Weimberg/Dahms pathway / [2Fe-2S] cluster
Function / homology
Function and homology information


L-arabinonate dehydratase / D-fuconate dehydratase / D-fuconate dehydratase activity / L-arabinonate dehydratase activity / galactonate dehydratase / galactonate dehydratase activity / arabinose catabolic process / 2 iron, 2 sulfur cluster binding / metal ion binding
Similarity search - Function
: / Dihydroxy-acid/6-phosphogluconate dehydratase / IlvD/EDD, N-terminal domain / Dihydroxy-acid dehydratase, C-terminal / Dihydroxy-acid/6-phosphogluconate dehydratase N-terminal
Similarity search - Domain/homology
2-KETOBUTYRIC ACID / FE2/S2 (INORGANIC) CLUSTER / L-arabinonate dehydratase
Similarity search - Component
Biological speciesRhizobium leguminosarum bv. trifolii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.44 Å
AuthorsRen, Y. / Rouvinen, J. / Hakulinen, N.
Funding support Finland, 1items
OrganizationGrant numberCountry
Academy of Finland322610 Finland
CitationJournal: Appl.Microbiol.Biotechnol. / Year: 2024
Title: Unveiling the importance of the C-terminus in the sugar acid dehydratase of the IlvD/EDD superfamily.
Authors: Ren, Y. / Vettenranta, E. / Penttinen, L. / Blomster Andberg, M. / Koivula, A. / Rouvinen, J. / Hakulinen, N.
History
DepositionApr 2, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 25, 2024Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: L-arabinonate dehydratase
B: L-arabinonate dehydratase
C: L-arabinonate dehydratase
D: L-arabinonate dehydratase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)256,23813
Polymers255,3364
Non-polymers9039
Water7,764431
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: mass spectrometry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area23570 Å2
ΔGint-200 kcal/mol
Surface area64540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)107.947, 148.211, 165.025
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

-
Components

#1: Protein
L-arabinonate dehydratase / ArDHT / D-fuconate dehydratase / Galactonate dehydratase / L-arabonate dehydratase


Mass: 63833.945 Da / Num. of mol.: 4 / Mutation: H579L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhizobium leguminosarum bv. trifolii (bacteria)
Gene: araD, Rleg2_2909 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: B5ZZ34, L-arabinonate dehydratase, D-fuconate dehydratase, galactonate dehydratase
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-FES / FE2/S2 (INORGANIC) CLUSTER


Mass: 175.820 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Fe2S2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-2KT / 2-KETOBUTYRIC ACID / 2-OXOBUTANOIC ACID


Mass: 102.089 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H6O3 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 431 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.6 Å3/Da / Density % sol: 52 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 100mM DTT (Dithiothreitol), 14 % (w/v) PEG 10000, 200 mM Ammonium acetate, 100 mM Tris, pH 8.5

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.87313 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jul 6, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.87313 Å / Relative weight: 1
ReflectionResolution: 2.44→48.48 Å / Num. obs: 98251 / % possible obs: 99.6 % / Redundancy: 6.9 % / Biso Wilson estimate: 38.73 Å2 / CC1/2: 0.986 / Net I/σ(I): 5.66
Reflection shellResolution: 2.44→2.53 Å / Num. unique obs: 9397 / CC1/2: 0.45

-
Processing

Software
NameVersionClassification
PHENIX1.19.1_4122refinement
PHENIX1.19.1_4122refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.44→48.48 Å / SU ML: 0.3338 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.3831
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2367 1999 2.04 %
Rwork0.1851 96219 -
obs0.186 98218 99.64 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 42.54 Å2
Refinement stepCycle: LAST / Resolution: 2.44→48.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17388 0 27 431 17846
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.007917766
X-RAY DIFFRACTIONf_angle_d0.991124063
X-RAY DIFFRACTIONf_chiral_restr0.05172678
X-RAY DIFFRACTIONf_plane_restr0.0083154
X-RAY DIFFRACTIONf_dihedral_angle_d7.71492507
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.44-2.50.32891340.28986462X-RAY DIFFRACTION95.57
2.5-2.570.33321420.26676847X-RAY DIFFRACTION99.97
2.57-2.650.3271430.26136813X-RAY DIFFRACTION99.96
2.65-2.730.31511410.25866819X-RAY DIFFRACTION99.99
2.73-2.830.29441410.23736846X-RAY DIFFRACTION99.94
2.83-2.940.30251430.23636848X-RAY DIFFRACTION99.94
2.94-3.080.29341420.22846845X-RAY DIFFRACTION99.94
3.08-3.240.2571420.21166863X-RAY DIFFRACTION99.97
3.24-3.440.24591430.19026882X-RAY DIFFRACTION99.99
3.44-3.710.25221440.17016888X-RAY DIFFRACTION99.96
3.71-4.080.20611430.14816907X-RAY DIFFRACTION100
4.08-4.670.16811440.13116954X-RAY DIFFRACTION99.96
4.67-5.880.20411460.15436993X-RAY DIFFRACTION99.94

+
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