[English] 日本語
Yorodumi
- PDB-1ywk: Crystal structure of 4-deoxy-1-threo-5-hexosulose-uronate ketol-i... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1ywk
TitleCrystal structure of 4-deoxy-1-threo-5-hexosulose-uronate ketol-isomerase from Enterococcus faecalis
Components4-deoxy-L-threo-5-hexosulose-uronate ketol-isomerase 1
KeywordsISOMERASE / Structural genomics / NYSGXRC target T1814 / ketol-isomerase / PSI / Protein Structure Initiative / New York SGX Research Center for Structural Genomics
Function / homology
Function and homology information


5-dehydro-4-deoxy-D-glucuronate isomerase / 4-deoxy-L-threo-5-hexosulose-uronate ketol-isomerase activity / pectin catabolic process / zinc ion binding
Similarity search - Function
5-keto 4-deoxyuronate isomerase / 5-keto-4-deoxyuronate isomerase, N-terminal / KduI/IolB isomerase / KduI/IolB family / RmlC-like cupin domain superfamily / Jelly Rolls / RmlC-like jelly roll fold / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
4-deoxy-L-threo-5-hexosulose-uronate ketol-isomerase 1
Similarity search - Component
Biological speciesEnterococcus faecalis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.95 Å
AuthorsFedorov, A.A. / Fedorov, E.V. / Almo, S.C. / Burley, S.K. / New York SGX Research Center for Structural Genomics (NYSGXRC)
CitationJournal: To be Published
Title: Crystal structure of 4-deoxy-1-threo-5-hexosulose-uronate ketol-isomerase from Enterococcus faecalis V583
Authors: Fedorov, A.A. / Fedorov, E.V. / Almo, S.C.
History
DepositionFeb 18, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 1, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 3, 2021Group: Database references / Structure summary / Category: audit_author / struct_ref_seq_dif
Item: _audit_author.identifier_ORCID / _struct_ref_seq_dif.details
Revision 1.4Feb 14, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: 4-deoxy-L-threo-5-hexosulose-uronate ketol-isomerase 1
B: 4-deoxy-L-threo-5-hexosulose-uronate ketol-isomerase 1
C: 4-deoxy-L-threo-5-hexosulose-uronate ketol-isomerase 1
D: 4-deoxy-L-threo-5-hexosulose-uronate ketol-isomerase 1
E: 4-deoxy-L-threo-5-hexosulose-uronate ketol-isomerase 1
F: 4-deoxy-L-threo-5-hexosulose-uronate ketol-isomerase 1


Theoretical massNumber of molelcules
Total (without water)200,2246
Polymers200,2246
Non-polymers00
Water0
1
A: 4-deoxy-L-threo-5-hexosulose-uronate ketol-isomerase 1


Theoretical massNumber of molelcules
Total (without water)33,3711
Polymers33,3711
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: 4-deoxy-L-threo-5-hexosulose-uronate ketol-isomerase 1


Theoretical massNumber of molelcules
Total (without water)33,3711
Polymers33,3711
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: 4-deoxy-L-threo-5-hexosulose-uronate ketol-isomerase 1


Theoretical massNumber of molelcules
Total (without water)33,3711
Polymers33,3711
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: 4-deoxy-L-threo-5-hexosulose-uronate ketol-isomerase 1


Theoretical massNumber of molelcules
Total (without water)33,3711
Polymers33,3711
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: 4-deoxy-L-threo-5-hexosulose-uronate ketol-isomerase 1


Theoretical massNumber of molelcules
Total (without water)33,3711
Polymers33,3711
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: 4-deoxy-L-threo-5-hexosulose-uronate ketol-isomerase 1


Theoretical massNumber of molelcules
Total (without water)33,3711
Polymers33,3711
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)81.010, 107.685, 191.021
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein
4-deoxy-L-threo-5-hexosulose-uronate ketol-isomerase 1 / / 5-keto-4-deoxyuronate isomerase 1 / DKI isomerase 1


Mass: 33370.648 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterococcus faecalis (bacteria) / Gene: kduI1, kduI-1 / Production host: Escherichia coli (E. coli)
References: UniProt: Q838L9, 5-dehydro-4-deoxy-D-glucuronate isomerase

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.08 Å3/Da / Density % sol: 38.6 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 5.5
Details: PEG 3350, sodium acetate, pH 5.5, VAPOR DIFFUSION, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X9A / Wavelength: 0.979 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Sep 22, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.95→25 Å / Num. all: 34809 / Num. obs: 34809 / % possible obs: 96.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -0 / Biso Wilson estimate: 78.4 Å2
Reflection shellResolution: 2.95→3.06 Å / % possible all: 90.7

-
Processing

Software
NameVersionClassification
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.95→24.9 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 190603.19 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.265 1722 4.9 %RANDOM
Rwork0.241 ---
all0.245 34809 --
obs0.241 34809 96.9 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 15.1418 Å2 / ksol: 0.297073 e/Å3
Displacement parametersBiso mean: 41 Å2
Baniso -1Baniso -2Baniso -3
1-2.5 Å20 Å20 Å2
2--8.64 Å20 Å2
3----11.14 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.43 Å0.38 Å
Luzzati d res low-5 Å
Luzzati sigma a0.56 Å0.5 Å
Refinement stepCycle: LAST / Resolution: 2.95→24.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12252 0 0 0 12252
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d26.3
X-RAY DIFFRACTIONc_improper_angle_d0.84
X-RAY DIFFRACTIONc_mcbond_it2.251.5
X-RAY DIFFRACTIONc_mcangle_it3.712
X-RAY DIFFRACTIONc_scbond_it3.62
X-RAY DIFFRACTIONc_scangle_it5.862.5
LS refinement shellResolution: 2.95→3.06 Å / Rfactor Rfree error: 0.03 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.376 162 5.1 %
Rwork0.343 3043 -
obs--90.7 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3ION.PARAMION.TOP

+
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