[English] 日本語
Yorodumi
- PDB-7e64: The crystal structure of peptidoglycan peptidase in complex with ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7.0E+64
TitleThe crystal structure of peptidoglycan peptidase in complex with inhibitor 2-2
ComponentsPeptidase M23
KeywordsHYDROLASE/INHIBITOR / HYDROLASE-INHIBITOR COMPLEX
Function / homologyGlucose Permease (Domain IIA) / Glucose Permease (Domain IIA) / Peptidase M23 / Peptidase family M23 / Duplicated hybrid motif / Distorted Sandwich / Mainly Beta / Chem-HWX / Peptidase M23
Function and homology information
Biological speciesCampylobacter jejuni (Campylobacter)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsChoi, Y. / Min, K.J. / Yoon, H.J. / Lee, H.H.
Funding support Korea, Republic Of, 1items
OrganizationGrant numberCountry
National Research Foundation (NRF, Korea)2015R1A5A1008958 Korea, Republic Of
CitationJournal: Commun Biol / Year: 2022
Title: Structure-based inhibitor design for reshaping bacterial morphology
Authors: Choi, Y. / Park, J.S. / Kim, J. / Min, K. / Mahasenan, K. / Kim, C. / Yoon, H.J. / Lim, S. / Cheon, D.H. / Lee, Y. / Ryu, S. / Mobashery, S. / Kim, B.M. / Lee, H.H.
History
DepositionFeb 21, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 23, 2022Provider: repository / Type: Initial release
Revision 1.1Aug 31, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Peptidase M23
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,8333
Polymers28,4641
Non-polymers3702
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: isothermal titration calorimetry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area13770 Å2
Unit cell
Length a, b, c (Å)116.140, 116.140, 57.820
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number169
Space group name H-MP61

-
Components

#1: Protein Peptidase M23


Mass: 28463.752 Da / Num. of mol.: 1 / Mutation: H247A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Campylobacter jejuni (Campylobacter) / Gene: A8118_01115 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A1J6PWI8
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-HWX / 2-[[(3S)-3-acetamido-4-[[(2R)-1-(oxidanylamino)-1-oxidanylidene-propan-2-yl]amino]-4-oxidanylidene-butyl]amino]ethanoic acid


Mass: 304.300 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H20N4O6 / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.95 Å3/Da / Density % sol: 68.9 %
Crystal growTemperature: 296 K / Method: vapor diffusion, sitting drop
Details: 0.2 M potassium sodium tartrate tetrahydrate, 0.1 M sodium citrate tribasic dihydrate pH 5.6 and 2 M ammonium sulfate

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jul 22, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.9→29.03 Å / Num. obs: 19252 / % possible obs: 99.6 % / Redundancy: 5.302 % / Biso Wilson estimate: 63.228 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.127 / Rrim(I) all: 0.141 / Χ2: 0.831 / Net I/σ(I): 10.97 / Num. measured all: 102079
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
2.9-3.075.2590.8752.0615903307430240.720.97198.4
3.07-3.285.2410.5023.5915263291329120.8980.558100
3.28-3.545.0380.2686.2813678271527150.9580.3100
3.54-3.885.5870.1721014096252325230.9820.19100
3.88-4.325.5420.11414.4112552226522650.990.126100
4.32-4.975.4120.08219.1710883201120110.9930.092100
4.97-6.055.1380.08618.098611167616760.9920.096100
6.05-8.375.0220.0720.416740134313420.9960.07899.9
8.37-29.035.5520.05329.6843538007840.9970.05998

-
Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
HKL-2000data scaling
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6JMZ

6jmz


Resolution: 2.9→29.03 Å / Cor.coef. Fo:Fc: 0.925 / Cor.coef. Fo:Fc free: 0.92 / SU B: 15.779 / SU ML: 0.283 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.835 / ESU R Free: 0.326 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2388 501 5 %RANDOM
Rwork0.2324 ---
obs0.2327 9519 99.88 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 86.6 Å2 / Biso mean: 64.861 Å2 / Biso min: 56.07 Å2
Baniso -1Baniso -2Baniso -3
1--0.91 Å2-0.46 Å2-0 Å2
2---0.91 Å20 Å2
3---2.96 Å2
Refinement stepCycle: final / Resolution: 2.9→29.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2014 0 22 0 2036
Biso mean--71.4 --
Num. residues----255
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.0192080
X-RAY DIFFRACTIONr_bond_other_d0.0010.022044
X-RAY DIFFRACTIONr_angle_refined_deg0.9121.9762797
X-RAY DIFFRACTIONr_angle_other_deg0.63434724
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5315254
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.44224.94489
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.06815376
X-RAY DIFFRACTIONr_dihedral_angle_4_deg5.92155
X-RAY DIFFRACTIONr_chiral_restr0.0540.2302
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.0212331
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02473
LS refinement shellResolution: 2.9→2.975 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.352 36 -
Rwork0.377 681 -
all-717 -
obs--99.86 %

+
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