[English] 日本語
Yorodumi
- PDB-4u8e: Crystal structure of 4-deoxy-L-threo-5-hexosulose-uronate ketol-i... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4u8e
TitleCrystal structure of 4-deoxy-L-threo-5-hexosulose-uronate ketol-isomerase from Streptococcus agalactiae
ComponentsPutative uncharacterized protein gbs1892
KeywordsISOMERASE / glycosaminoglycan metabolism / rossman fold / 4-deoxy-L-threo-5-hexosulose-uronate
Function / homology
Function and homology information


lactose metabolic process / intramolecular oxidoreductase activity, interconverting aldoses and ketoses
Similarity search - Function
Ribose-5-phosphate isomerase, C-terminal / Ribose-5-phosphate isomerase / Sugar-phosphate isomerase, RpiB/LacA/LacB family / Sugar-phosphate isomerase, RpiB/LacA/LacB superfamily / Ribose/Galactose Isomerase / Ribose 5-phosphate Isomerase B; Chain: A, / Sugar-phosphate isomerase, RpiB/LacA/LacB / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Ribose-5-phosphate isomerase C-terminal domain-containing protein
Similarity search - Component
Biological speciesStreptococcus agalactiae NEM316 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2 Å
AuthorsMaruyama, y. / Oiki, S. / Takase, R. / Mikami, B. / Murata, K. / Hashimoto, W.
Funding support Japan, 3items
OrganizationGrant numberCountry
Grants-in-Aid for Scientific Research from the Japan Society for the Promotion of Science Japan
Targeted Proteins Research Program from the Ministry of Education, Culture, Sports, Science, and Technology (MEXT) of Japan Japan
Research Grant from Mizutani Foundation for Glycoscience Japan
CitationJournal: J.Biol.Chem. / Year: 2015
Title: Metabolic Fate of Unsaturated Glucuronic/Iduronic Acids from Glycosaminoglycans: MOLECULAR IDENTIFICATION AND STRUCTURE DETERMINATION OF STREPTOCOCCAL ISOMERASE AND DEHYDROGENASE
Authors: Maruyama, Y. / Oiki, S. / Takase, R. / Mikami, B. / Murata, K. / Hashimoto, W.
History
DepositionAug 3, 2014Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jan 21, 2015Provider: repository / Type: Initial release
Revision 1.1Feb 4, 2015Group: Database references
Revision 1.2Feb 11, 2015Group: Database references
Revision 1.3Apr 1, 2015Group: Database references
Revision 1.4Jan 29, 2020Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Source and taxonomy
Category: citation / diffrn_source ...citation / diffrn_source / entity_src_gen / pdbx_struct_oper_list / pdbx_validate_close_contact
Item: _citation.journal_id_CSD / _diffrn_source.pdbx_synchrotron_site ..._citation.journal_id_CSD / _diffrn_source.pdbx_synchrotron_site / _entity_src_gen.pdbx_alt_source_flag / _pdbx_struct_oper_list.symmetry_operation
Revision 1.5Nov 8, 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
Revision 1.6Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Putative uncharacterized protein gbs1892


Theoretical massNumber of molelcules
Total (without water)24,6001
Polymers24,6001
Non-polymers00
Water2,180121
1
A: Putative uncharacterized protein gbs1892

A: Putative uncharacterized protein gbs1892

A: Putative uncharacterized protein gbs1892

A: Putative uncharacterized protein gbs1892


Theoretical massNumber of molelcules
Total (without water)98,3994
Polymers98,3994
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_555-x,y,-z1
crystal symmetry operation4_555x,-y,-z1
Buried area10990 Å2
ΔGint-76 kcal/mol
Surface area30720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.234, 87.968, 90.295
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11A-345-

HOH

21A-347-

HOH

-
Components

#1: Protein Putative uncharacterized protein gbs1892


Mass: 24599.646 Da / Num. of mol.: 1 / Mutation: T74A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus agalactiae NEM316 (bacteria)
Strain: NEM316 / Gene: gbs1892 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q8E369
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 121 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 2.15 Å3/Da / Density % sol: 42.75 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 15% polyethylene glycol 10,000, 2% dioxane, and 0.1 M sodium citrate (pH 6.5)

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL38B1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 18, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 14717 / % possible obs: 100 % / Redundancy: 6 % / Net I/σ(I): 28.6

-
Processing

SoftwareName: REFMAC / Version: 5.8.0049 / Classification: refinement
RefinementStarting model: 2PPW

2ppw


Resolution: 2→45.15 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.925 / SU B: 4.031 / SU ML: 0.112 / Cross valid method: THROUGHOUT / ESU R: 0.188 / ESU R Free: 0.164 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22491 737 5 %RANDOM
Rwork0.17942 ---
obs0.18164 13926 99.05 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 27.179 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å20 Å2-0 Å2
2---0.05 Å20 Å2
3---0.06 Å2
Refinement stepCycle: 1 / Resolution: 2→45.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1656 0 0 121 1777
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0191705
X-RAY DIFFRACTIONr_bond_other_d0.0010.021603
X-RAY DIFFRACTIONr_angle_refined_deg0.9341.9652305
X-RAY DIFFRACTIONr_angle_other_deg0.7233695
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.4845219
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.77725.47684
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.37815293
X-RAY DIFFRACTIONr_dihedral_angle_4_deg26.866156
X-RAY DIFFRACTIONr_chiral_restr0.0530.2249
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.021990
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02402
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.7432.623855
X-RAY DIFFRACTIONr_mcbond_other0.7422.621854
X-RAY DIFFRACTIONr_mcangle_it1.2443.9281069
X-RAY DIFFRACTIONr_mcangle_other1.2433.9311070
X-RAY DIFFRACTIONr_scbond_it0.8222.789850
X-RAY DIFFRACTIONr_scbond_other0.8212.783848
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.4264.1291232
X-RAY DIFFRACTIONr_long_range_B_refined2.83921.3142048
X-RAY DIFFRACTIONr_long_range_B_other2.74121.0861997
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.996→2.048 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.274 41 -
Rwork0.235 949 -
obs--91.67 %

+
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