[English] 日本語
Yorodumi
- PDB-6jn0: Structure of H247A mutant peptidoglycan peptidase complex with te... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6jn0
TitleStructure of H247A mutant peptidoglycan peptidase complex with tetra-tri peptide
Components
  • C0O-DAL-API
  • Peptidase M23
KeywordsHYDROLASE / Peptidoglycan
Function / homologyGlucose Permease (Domain IIA) / Glucose Permease (Domain IIA) / Peptidase M23 / Peptidase family M23 / Duplicated hybrid motif / Distorted Sandwich / Mainly Beta / polypeptide(D) / Peptidase M23
Function and homology information
Biological speciesCampylobacter jejuni (Campylobacter)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.164 Å
AuthorsMin, K.J. / An, D.R. / Yoon, H.J. / Suh, S.W. / Lee, H.H.
Funding support Korea, Republic Of, United States, 8items
OrganizationGrant numberCountry
National Research Foundation (Korea)2015R1A5A1008958 Korea, Republic Of
National Research Foundation (Korea)2015R1C1A1A01054842 Korea, Republic Of
National Research Foundation (Korea)2018R1A2B2008142 Korea, Republic Of
Ministry of Science, ICT and Future Planning2014M1A8A1049296 Korea, Republic Of
Ministry of Science, ICT and Future Planning2013R1A2A1A05067303 Korea, Republic Of
National Research Foundation (Korea)2018R1D1A1B07040808 Korea, Republic Of
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI090348 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM61629 United States
CitationJournal: Nat Commun / Year: 2020
Title: Peptidoglycan reshaping by a noncanonical peptidase for helical cell shape in Campylobacter jejuni.
Authors: Min, K. / An, D.R. / Yoon, H.J. / Rana, N. / Park, J.S. / Kim, J. / Lee, M. / Hesek, D. / Ryu, S. / Kim, B.M. / Mobashery, S. / Suh, S.W. / Lee, H.H.
History
DepositionMar 13, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 15, 2020Provider: repository / Type: Initial release
Revision 1.1Feb 5, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Mar 23, 2022Group: Author supporting evidence / Database references / Derived calculations
Category: database_2 / pdbx_audit_support ...database_2 / pdbx_audit_support / struct_conn / struct_conn_type
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_audit_support.funding_organization / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn_type.id
Revision 2.0Apr 5, 2023Group: Atomic model / Derived calculations ...Atomic model / Derived calculations / Polymer sequence / Source and taxonomy / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / entity / entity_poly / entity_poly_seq / pdbx_entity_src_syn / pdbx_poly_seq_scheme / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / struct_conn
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.type_symbol / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_auth_comp_id / _atom_site_anisotrop.pdbx_label_atom_id / _atom_site_anisotrop.pdbx_label_comp_id / _atom_site_anisotrop.type_symbol / _entity.pdbx_description / _entity_poly.pdbx_seq_one_letter_code / _entity_poly.pdbx_seq_one_letter_code_can / _entity_poly_seq.mon_id / _pdbx_entity_src_syn.pdbx_beg_seq_num / _pdbx_entity_src_syn.pdbx_end_seq_num / _pdbx_poly_seq_scheme.mon_id / _pdbx_poly_seq_scheme.pdb_mon_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_label_comp_id
Revision 3.0Nov 15, 2023Group: Atomic model / Data collection / Derived calculations
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp_atom / chem_comp_bond / struct_conn
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_label_atom_id / _struct_conn.ptnr1_label_atom_id
Revision 3.1Mar 20, 2024Group: Derived calculations
Category: pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop
Item: _pdbx_struct_assembly.details / _pdbx_struct_assembly.method_details ..._pdbx_struct_assembly.details / _pdbx_struct_assembly.method_details / _pdbx_struct_assembly.oligomeric_count / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_gen.asym_id_list

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Peptidase M23
B: C0O-DAL-API
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,9613
Polymers28,8952
Non-polymers651
Water2,828157
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)114.796, 114.796, 55.621
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: Polypeptide(D) C0O-DAL-API


Mass: 431.441 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 157 / 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: 3.68 Å3/Da / Density % sol: 66.56 %
Crystal growTemperature: 296 K / Method: vapor diffusion, sitting drop / Details: 1.8 M ammonium citrate tribasic at pH 7.0

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Dec 23, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.95→50 Å / Num. obs: 22451 / % possible obs: 99 % / Redundancy: 2.4 % / Rmerge(I) obs: 0.057 / Rpim(I) all: 0.046 / Rrim(I) all: 0.073 / Χ2: 2.727 / Net I/σ(I): 15.3
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.95-1.982.10.32828110.8280.2730.4281.76293.2
1.98-2.022.40.30329200.8440.2460.3911.82199.4
2.02-2.062.40.25429330.8860.2030.3261.90299.9
2.06-2.12.40.21929510.9070.1770.2831.999100
2.1-2.152.50.1929650.9240.1520.2442.058100
2.15-2.22.50.17729450.9330.1420.2282.201100
2.2-2.252.50.14929480.9470.1190.1912.328100
2.25-2.312.50.13430110.960.1070.1722.258100
2.31-2.382.50.11929200.9650.0960.1542.294100
2.38-2.462.50.10829200.9730.0870.1392.475100
2.46-2.542.50.09830050.9770.0780.1262.554100
2.54-2.652.50.08729530.9790.0690.1122.838100
2.65-2.772.50.07329300.9830.0580.0932.767100
2.77-2.912.50.06629520.9870.0520.0842.982100
2.91-3.12.50.06329710.9860.050.0813.47899.9
3.1-3.332.50.05529410.990.0440.0713.683100
3.33-3.672.50.04929610.9910.0390.0633.88699.7
3.67-4.22.50.04629300.9910.0370.0594.03199.2
4.2-5.292.40.04228740.9920.0340.0543.83297.3
5.29-502.30.04126810.9910.0340.0533.2590.7

-
Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIX1.13_2998refinement
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.164→31.136 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 18.65
RfactorNum. reflection% reflection
Rfree0.1992 1065 4.75 %
Rwork0.1611 --
obs0.1628 22429 99.76 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 165.12 Å2 / Biso mean: 47.7668 Å2 / Biso min: 18.89 Å2
Refinement stepCycle: final / Resolution: 2.164→31.136 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2014 0 31 157 2202
Biso mean--76.58 54.58 -
Num. residues----255
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.1642-2.26270.22361420.1678258198
2.2627-2.38190.18771560.16372640100
2.3819-2.53110.1954950.16752712100
2.5311-2.72640.18181190.1722659100
2.7264-3.00060.21361590.17482630100
3.0006-3.43430.22381280.16632701100
3.4343-4.3250.15611340.13982691100
4.325-31.1360.22541320.1662750100
Refinement TLS params.Method: refined / Origin x: 22.0325 Å / Origin y: 44.6916 Å / Origin z: -0.3762 Å
111213212223313233
T0.1921 Å20.055 Å2-0.0129 Å2-0.2521 Å20.039 Å2--0.2175 Å2
L1.021 °2-0.3876 °2-0.5035 °2-0.6894 °20.526 °2--2.2267 °2
S-0.0543 Å °-0.082 Å °-0.0067 Å °0.0867 Å °0.0951 Å °0.0456 Å °0.2796 Å °-0.0741 Å °0.0024 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA20 - 274
2X-RAY DIFFRACTION1allA300
3X-RAY DIFFRACTION1allC301
4X-RAY DIFFRACTION1allS1 - 174

+
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