[English] 日本語
Yorodumi
- PDB-5wly: E. coli LpxH- 8 mutations -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5wly
TitleE. coli LpxH- 8 mutations
ComponentsUDP-2,3-diacylglucosamine hydrolase
KeywordsHYDROLASE / lipid A synthesis / open conformation / UDP-diacyl-glucosamine pyrophosphohydrolase / apha/beta-hydrolase
Function / homology
Function and homology information


UDP-2,3-diacylglucosamine diphosphatase / UDP-2,3-diacylglucosamine hydrolase activity / lipid A biosynthetic process / extrinsic component of plasma membrane / manganese ion binding / cytoplasm
Similarity search - Function
UDP-2,3-diacylglucosamine hydrolase / UDP-2,3-diacylglucosamine hydrolase LpxH-like / Calcineurin-like phosphoesterase domain, ApaH type / Calcineurin-like phosphoesterase / Metallo-dependent phosphatase-like
Similarity search - Domain/homology
FORMIC ACID / : / UDP-2,3-diacylglucosamine hydrolase / UDP-2,3-diacylglucosamine hydrolase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsBohl, T.E. / Aihara, H. / Shi, K. / Lee, J.K.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM118047 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)P41-GM103403 United States
Department of Energy (DOE, United States)DE-AC02-06CH11357 United States
CitationJournal: J. Biol. Chem. / Year: 2018
Title: The substrate-binding cap of the UDP-diacylglucosamine pyrophosphatase LpxH is highly flexible, enabling facile substrate binding and product release.
Authors: Bohl, T.E. / Ieong, P. / Lee, J.K. / Lee, T. / Kankanala, J. / Shi, K. / Demir, O. / Kurahashi, K. / Amaro, R.E. / Wang, Z. / Aihara, H.
History
DepositionJul 28, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 11, 2018Provider: repository / Type: Initial release
Revision 1.1Apr 18, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.pdbx_database_id_DOI ..._citation.journal_abbrev / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Jun 6, 2018Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / citation ...chem_comp / citation / entity / pdbx_entity_nonpoly
Item: _chem_comp.name / _citation.journal_volume ..._chem_comp.name / _citation.journal_volume / _citation.page_first / _citation.page_last / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Revision 1.3Jul 11, 2018Group: Data collection / Structure summary / Category: struct / Item: _struct.title
Revision 1.4Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support
Revision 1.5Oct 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: UDP-2,3-diacylglucosamine hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,9856
Polymers27,7321
Non-polymers2535
Water2,684149
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: UDP-2,3-diacylglucosamine hydrolase
hetero molecules

A: UDP-2,3-diacylglucosamine hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,97112
Polymers55,4642
Non-polymers50710
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,y,-z1
Buried area4210 Å2
ΔGint-66 kcal/mol
Surface area18920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.012, 62.064, 66.047
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21221
Space group name HallP22ab(y,z,x)
Symmetry operation#1: x,y,z
#2: x+1/2,-y,-z+1/2
#3: -x,y,-z
#4: -x+1/2,-y,z+1/2
Components on special symmetry positions
IDModelComponents
11A-402-

HOH

Detailsmonomer by gel filtration

-
Components

-
Protein , 1 types, 1 molecules A

#1: Protein UDP-2,3-diacylglucosamine hydrolase / UDP-2 / 3-diacylglucosamine diphosphatase


Mass: 27731.977 Da / Num. of mol.: 1
Mutation: F141H, L142S, L146S, F147H, E14A, E15A, K161T, E162A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: DH5alpha
Gene: lpxH, AUQ13_20415, BK337_17315, BUE81_23120, EC3234A_5c00260, PGD_02789
Plasmid: pET24+ / Details (production host): short C-terminal His-tag / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL-21 DE3
References: UniProt: Q0P6L0, UniProt: P43341*PLUS, UDP-2,3-diacylglucosamine diphosphatase

-
Non-polymers , 5 types, 154 molecules

#2: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CH2O2
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 149 / 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: 2.11 Å3/Da / Density % sol: 41.71 % / Description: parallelogram shaped plate crystals
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 8.2
Details: 7.1 g/L protein in 0.25 M NaCl, 10 mM Tris-HCl pH 7.4, 2.5 mM DTT, 1.25 mM MnCl2, and 20 mM reduced glutathione was combined 2:1 (protein to well solution) with 0.1 M Tris-HCl pH 8.2, 80 mM ...Details: 7.1 g/L protein in 0.25 M NaCl, 10 mM Tris-HCl pH 7.4, 2.5 mM DTT, 1.25 mM MnCl2, and 20 mM reduced glutathione was combined 2:1 (protein to well solution) with 0.1 M Tris-HCl pH 8.2, 80 mM magnesium formate, and 5% 2-propanol

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97918 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 22, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2→66.05 Å / Num. obs: 16046 / % possible obs: 98.6 % / Redundancy: 6 % / CC1/2: 0.994 / Rmerge(I) obs: 0.179 / Rpim(I) all: 0.078 / Net I/σ(I): 7.7
Reflection shellResolution: 2→2.06 Å / Redundancy: 5.9 % / Rmerge(I) obs: 1.973 / Mean I/σ(I) obs: 0.8 / Num. unique obs: 1090 / CC1/2: 0.279 / Rpim(I) all: 0.867 / % possible all: 91

-
Processing

Software
NameVersionClassification
PHENIXv1.11.1_2575refinement
Cootv0.8.7model building
Aimlessv0.5.21data scaling
PHENIXv1.11.1_2575phasing
XDSvOct 15, 2015data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5B4A

5b4a


Resolution: 2→45.23 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / Phase error: 26.93
RfactorNum. reflection% reflection
Rfree0.2271 689 4.67 %
Rwork0.1983 --
obs0.1998 14750 90.44 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 42.45 Å2
Refinement stepCycle: LAST / Resolution: 2→45.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1687 0 10 149 1846
LS refinement shellResolution: 2→2.16 Å
RfactorNum. reflection% reflection
Rfree0.3626 117 4.85 %
Rwork0.331 2414 -
obs--71.09 %

+
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