[English] 日本語
Yorodumi
- PDB-5utp: Crystal structure of Burkholderia cenocepacia family 3 glycoside ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5utp
TitleCrystal structure of Burkholderia cenocepacia family 3 glycoside hydrolase (NagZ) bound to N-ethylbutyryl-PUGNAc
ComponentsBeta-hexosaminidase
KeywordsHYDROLASE/HYDROLASE INHIBITOR / Glycoside hydrolase / family 3 / NagZ / HYDROLASE-HYDROLASE INHIBITOR complex
Function / homology
Function and homology information


beta-N-acetylhexosaminidase activity / beta-N-acetylhexosaminidase / peptidoglycan turnover / peptidoglycan biosynthetic process / cell wall organization / regulation of cell shape / carbohydrate metabolic process / cell division / cytoplasm
Similarity search - Function
Beta-hexosaminidase, bacterial / : / Glycoside hydrolase, family 3, N-terminal domain / Glycoside hydrolase, family 3, N-terminal / Glycoside hydrolase, family 3, N-terminal domain superfamily / Glycosyl hydrolase family 3 N terminal domain / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
Chem-8M7 / Beta-hexosaminidase / Beta-hexosaminidase
Similarity search - Component
Biological speciesBurkholderia cenocepacia (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsVadlamani, G. / Mark, B.L.
CitationJournal: Protein Sci. / Year: 2017
Title: Conformational flexibility of the glycosidase NagZ allows it to bind structurally diverse inhibitors to suppress beta-lactam antibiotic resistance.
Authors: Vadlamani, G. / Stubbs, K.A. / Desire, J. / Bleriot, Y. / Vocadlo, D.J. / Mark, B.L.
History
DepositionFeb 15, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 19, 2017Provider: repository / Type: Initial release
Revision 1.1Jun 7, 2017Group: Database references
Revision 1.2Sep 27, 2017Group: Author supporting evidence / Category: pdbx_audit_support
Revision 1.3Oct 4, 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Beta-hexosaminidase
B: Beta-hexosaminidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,0524
Polymers76,2342
Non-polymers8192
Water7,098394
1
A: Beta-hexosaminidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,5262
Polymers38,1171
Non-polymers4091
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Beta-hexosaminidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,5262
Polymers38,1171
Non-polymers4091
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)51.210, 85.890, 65.610
Angle α, β, γ (deg.)90.00, 102.79, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein Beta-hexosaminidase / Beta-N-acetylhexosaminidase / N-acetyl-beta-glucosaminidase


Mass: 38116.766 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Burkholderia cenocepacia (bacteria) / Gene: nagZ, A3203_21235, WL84_04775 / Production host: Escherichia coli (E. coli)
References: UniProt: A0A125HFC0, UniProt: B4EA43*PLUS, beta-N-acetylhexosaminidase
#2: Chemical ChemComp-8M7 / N-[(2Z,3R,4R,5S,6R)-4,5-dihydroxy-6-(hydroxymethyl)-2-{[(phenylcarbamoyl)oxy]imino}tetrahydro-2H-pyran-3-yl]-2-ethylbutanamide


Mass: 409.434 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C19H27N3O7
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 394 / 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: 1.85 Å3/Da / Density % sol: 33.36 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 30-32% PEG8000, 0.1 M MES, pH 6.2-6.8 / PH range: 6.2-6.8

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Sep 25, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.2→49.94 Å / Num. obs: 27671 / % possible obs: 98.2 % / Redundancy: 2.9 % / CC1/2: 0.95 / Rmerge(I) obs: 0.137 / Net I/σ(I): 5.1
Reflection shellResolution: 2.2→2.27 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.249 / Mean I/σ(I) obs: 3.1 / Num. unique obs: 2380 / CC1/2: 0.908 / % possible all: 98

-
Processing

Software
NameVersionClassification
PHENIX(dev_2236)refinement
iMOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 4G6C

4g6c


Resolution: 2.2→25.23 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 21.82
RfactorNum. reflection% reflection
Rfree0.2258 --
Rwork0.1746 --
obs-27652 98.14 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.2→25.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5003 0 58 394 5455
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0025179
X-RAY DIFFRACTIONf_angle_d0.6237042
X-RAY DIFFRACTIONf_dihedral_angle_d16.723113
X-RAY DIFFRACTIONf_chiral_restr0.072829
X-RAY DIFFRACTIONf_plane_restr0.003914
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.2550.25211410.18911809X-RAY DIFFRACTION98
2.255-2.3160.26321420.18351823X-RAY DIFFRACTION98
2.316-2.38410.24581410.18081814X-RAY DIFFRACTION98
2.3841-2.4610.24141440.19161845X-RAY DIFFRACTION98
2.461-2.54880.29441420.18981820X-RAY DIFFRACTION99
2.5488-2.65080.2531430.18981834X-RAY DIFFRACTION99
2.6508-2.77130.24061440.18411838X-RAY DIFFRACTION99
2.7713-2.91720.26081440.18731846X-RAY DIFFRACTION99
2.9172-3.09960.22081430.19011843X-RAY DIFFRACTION99
3.0996-3.33850.22481450.17891854X-RAY DIFFRACTION99
3.3385-3.67350.23911440.16451850X-RAY DIFFRACTION99
3.6735-4.2030.17671420.15651838X-RAY DIFFRACTION98
4.203-5.28730.18091420.14771824X-RAY DIFFRACTION97

+
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