[English] 日本語
Yorodumi
- PDB-8syh: X-ray crystal structure of UDP-2,3-diacetamido-2,3-dideoxy-glucur... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8syh
TitleX-ray crystal structure of UDP-2,3-diacetamido-2,3-dideoxy-glucuronic acid-2-epimerase from Thermus thermophilus strain HB27, D98N variant in the presence of UDP-2,3-diacetamido-2,3-dideoxy-glucuronic acid and UDP at pH 8
ComponentsUDP-2,3-diacetamido-2,3-dideoxy-glucuronic acid-2-epimerase
KeywordsISOMERASE / lipopolysaccharide / O-antigen / 2-epimerase
Function / homologyUDP-N-acetylglucosamine 2-epimerase (non-hydrolysing) / UDP-N-acetylglucosamine 2-epimerase WecB-like / UDP-N-acetylglucosamine 2-epimerase activity / UDP-N-acetylglucosamine 2-epimerase domain / UDP-N-acetylglucosamine 2-epimerase / nucleotide binding / Chem-MJL / URIDINE-5'-DIPHOSPHATE / UDP-N-acetylglucosamine 2-epimerase
Function and homology information
Biological speciesThermus thermophilus HB27 (bacteria)
MethodX-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 2 Å
AuthorsJast, J.D.T. / Thoden, J.B. / Holden, H.M.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35 GM134643 United States
CitationJournal: J.Biol.Chem. / Year: 2023
Title: Structural analysis of a bacterial UDP-sugar 2-epimerase reveals the active site architecture before and after catalysis.
Authors: Thoden, J.B. / McKnight, J.O. / Kroft, C.W. / Jast, J.D.T. / Holden, H.M.
History
DepositionMay 25, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 13, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Database references / Category: citation / Item: _citation.journal_volume

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: UDP-2,3-diacetamido-2,3-dideoxy-glucuronic acid-2-epimerase
B: UDP-2,3-diacetamido-2,3-dideoxy-glucuronic acid-2-epimerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,1928
Polymers83,9882
Non-polymers2,2046
Water5,350297
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4430 Å2
ΔGint-44 kcal/mol
Surface area25890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.788, 128.158, 58.475
Angle α, β, γ (deg.)90.00, 112.54, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein UDP-2,3-diacetamido-2,3-dideoxy-glucuronic acid-2-epimerase


Mass: 41994.086 Da / Num. of mol.: 2 / Mutation: D98N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus HB27 (bacteria) / Strain: ATCC BAA-163 / DSM 7039 / HB27 / Gene: TT_C0285 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta2 / References: UniProt: Q72KY0
#2: Chemical ChemComp-MJL / (2~{S},3~{S},4~{R},5~{R},6~{R})-4,5-diacetamido-6-[[[(2~{R},3~{S},4~{R},5~{R})-5-[2,4-bis(oxidanylidene)pyrimidin-1-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]oxy-3-oxidanyl-oxane-2-carboxylic acid / UDP-2,3-diacetamido-2,3-dideoxy-alpha-D-glucuronate


Mass: 662.389 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C19H28N4O18P2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-UDP / URIDINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 404.161 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H14N2O12P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: UDP*YM
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 297 / 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: 2.34 Å3/Da / Density % sol: 47.44 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: Protein incubated with 5 mM UDP-2,3-diacetamido-2,3-dideoxy-glucuronic acid and 5 mM UDP. Precipitant used was 22-27% pentaerythritol propoxylate (5/4 PO/OH), 100 mM HEPPS (pH 8)

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SEALED TUBE / Type: BRUKER D8 QUEST / Wavelength: 1.5418 Å
DetectorType: Bruker PHOTON II / Detector: PIXEL / Date: Mar 11, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 51464 / % possible obs: 98.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.4 % / Rsym value: 0.09 / Net I/σ(I): 12.1
Reflection shellResolution: 2→2.1 Å / Redundancy: 3.3 % / Mean I/σ(I) obs: 2 / Num. unique obs: 6828 / Rsym value: 0.44 / % possible all: 96.6

-
Processing

Software
NameVersionClassification
REFMAC5.8.0403refinement
SAINTdata reduction
SADABSdata scaling
REFMACphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 2→40.59 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.928 / SU B: 6.044 / SU ML: 0.152 / Cross valid method: THROUGHOUT / ESU R: 0.188 / ESU R Free: 0.17 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23393 2710 5.3 %RANDOM
Rwork0.18294 ---
obs0.18557 48754 98.88 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 28.626 Å2
Baniso -1Baniso -2Baniso -3
1--0.02 Å2-0 Å2-0.01 Å2
2--0.03 Å2-0 Å2
3---0 Å2
Refinement stepCycle: 1 / Resolution: 2→40.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5665 0 138 297 6100
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0125954
X-RAY DIFFRACTIONr_bond_other_d0.0010.0165720
X-RAY DIFFRACTIONr_angle_refined_deg1.5971.6758102
X-RAY DIFFRACTIONr_angle_other_deg0.5461.58413132
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7155730
X-RAY DIFFRACTIONr_dihedral_angle_2_deg11.517554
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.276101008
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0770.2926
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.026973
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021347
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_it2.6492.7992896
X-RAY DIFFRACTIONr_mcbond_other2.6442.7992896
X-RAY DIFFRACTIONr_mcangle_it3.9075.0213619
X-RAY DIFFRACTIONr_mcangle_other3.9065.0223620
X-RAY DIFFRACTIONr_scbond_it3.3253.1463058
X-RAY DIFFRACTIONr_scbond_other3.3163.1413051
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.1445.6054479
X-RAY DIFFRACTIONr_long_range_B_refined6.5829.026762
X-RAY DIFFRACTIONr_long_range_B_other6.55528.876702
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.373 183 -
Rwork0.348 3480 -
obs--96.07 %

+
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