[English] 日本語
Yorodumi
- PDB-6g9f: Structural basis for the inhibition of E. coli PBP2 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6g9f
TitleStructural basis for the inhibition of E. coli PBP2
ComponentsPeptidoglycan D,D-transpeptidase MrdA
KeywordsHYDROLASE/ANTIBIOTIC / penicillin binding protein / HYDROLASE-ANTIBIOTIC COMPLEX
Function / homology
Function and homology information


peptidoglycan L,D-transpeptidase activity / serine-type D-Ala-D-Ala carboxypeptidase / serine-type D-Ala-D-Ala carboxypeptidase activity / penicillin binding / peptidoglycan biosynthetic process / cell wall organization / outer membrane-bounded periplasmic space / regulation of cell shape / response to antibiotic / proteolysis / plasma membrane
Similarity search - Function
Penicillin-binding protein 2 / Penicillin-binding protein, dimerisation domain / Penicillin-binding Protein dimerisation domain / Penicillin-binding protein, dimerisation domain superfamily / Penicillin-binding protein, transpeptidase / Penicillin binding protein transpeptidase domain / Beta-lactamase/transpeptidase-like
Similarity search - Domain/homology
Chem-NXL / Peptidoglycan D,D-transpeptidase MrdA
Similarity search - Component
Biological speciesEscherichia coli K-12 (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.35 Å
AuthorsRuff, M. / Levy, N.
CitationJournal: J.Med.Chem. / Year: 2019
Title: Structural Basis for E. coli Penicillin Binding Protein (PBP) 2 Inhibition, a Platform for Drug Design.
Authors: Levy, N. / Bruneau, J.M. / Le Rouzic, E. / Bonnard, D. / Le Strat, F. / Caravano, A. / Chevreuil, F. / Barbion, J. / Chasset, S. / Ledoussal, B. / Moreau, F. / Ruff, M.
History
DepositionApr 10, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 22, 2019Provider: repository / Type: Initial release
Revision 1.1Feb 5, 2020Group: Database references / Source and taxonomy
Category: entity_src_gen / struct_ref ...entity_src_gen / struct_ref / struct_ref_seq / struct_ref_seq_dif
Item: _entity_src_gen.pdbx_gene_src_gene / _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id ..._entity_src_gen.pdbx_gene_src_gene / _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id / _entity_src_gen.pdbx_gene_src_scientific_name / _struct_ref.db_code / _struct_ref.pdbx_db_accession / _struct_ref_seq.pdbx_db_accession / _struct_ref_seq_dif.pdbx_seq_db_accession_code

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Peptidoglycan D,D-transpeptidase MrdA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,0762
Polymers62,8091
Non-polymers2671
Water2,216123
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area24270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)125.078, 182.875, 74.767
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-734-

HOH

21A-770-

HOH

31A-796-

HOH

41A-808-

HOH

-
Components

#1: Protein Peptidoglycan D,D-transpeptidase MrdA / Penicillin-binding protein 2 / PBP-2


Mass: 62809.215 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: The Ser 330 in the structure is modified covalently and is named (S31)
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Gene: mrdA, pbpA, b0635, JW0630 / Production host: Escherichia coli BL21 (bacteria)
References: UniProt: P0AD65, serine-type D-Ala-D-Ala carboxypeptidase
#2: Chemical ChemComp-NXL / (2S,5R)-1-formyl-5-[(sulfooxy)amino]piperidine-2-carboxamide / avibactam, bound form, NXL104, bound form / Avibactam


Mass: 267.260 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H13N3O6S / Comment: antibiotic, inhibitor*YM
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 123 / 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: 3.38 Å3/Da / Density % sol: 63.56 %
Crystal growTemperature: 300 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.1 M TrisBase / Bicine pH 8,5 ; 0.1 M [Carboxylic acids mix (0.02 M Sodium formate ; 0.02 M Ammonium acetate ; 0.02 M Sodium citrate tribasic dihydrate ; 0.02 M Sodium potassium tartrate ...Details: 0.1 M TrisBase / Bicine pH 8,5 ; 0.1 M [Carboxylic acids mix (0.02 M Sodium formate ; 0.02 M Ammonium acetate ; 0.02 M Sodium citrate tribasic dihydrate ; 0.02 M Sodium potassium tartrate tetrahydrate ; 0.02 M Sodium oxamate) ; 24 % Glycerol ; 12 % PEG 4000] equilibrated against 2.0 M NaCl

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-X / Wavelength: 1.5418 Å
DetectorType: DECTRIS EIGER R 4M / Detector: PIXEL / Date: Feb 8, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.35→39.005 Å / Num. obs: 35810 / % possible obs: 98.67 % / Redundancy: 5.5 % / CC1/2: 0.996 / Rmerge(I) obs: 0.1454 / Rpim(I) all: 0.06713 / Rrim(I) all: 0.1607 / Net I/σ(I): 7.87
Reflection shellResolution: 2.35→2.434 Å / Redundancy: 5.6 % / Rmerge(I) obs: 2.546 / Num. unique obs: 3525 / CC1/2: 0.419 / Rpim(I) all: 1.167 / Rrim(I) all: 2.809 / % possible all: 95.57

-
Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6G9S
Resolution: 2.35→39.01 Å / SU ML: 0.36 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 28.04
RfactorNum. reflection% reflection
Rfree0.248 3754 5.6 %
Rwork0.199 --
obs0.201 35639 97.1 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.35→39.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4262 0 17 123 4402
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0084386
X-RAY DIFFRACTIONf_angle_d0.9715965
X-RAY DIFFRACTIONf_dihedral_angle_d6.2852622
X-RAY DIFFRACTIONf_chiral_restr0.053646
X-RAY DIFFRACTIONf_plane_restr0.007774
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3498-2.37950.36111040.31941817X-RAY DIFFRACTION77
2.3795-2.41080.31921290.32232203X-RAY DIFFRACTION89
2.4108-2.44380.3671350.32432208X-RAY DIFFRACTION94
2.4438-2.47870.42031440.31732394X-RAY DIFFRACTION98
2.4787-2.51570.31421390.30722419X-RAY DIFFRACTION99
2.5157-2.5550.33951400.31342368X-RAY DIFFRACTION99
2.555-2.59690.35361420.30442395X-RAY DIFFRACTION99
2.5969-2.64170.33351400.30252413X-RAY DIFFRACTION100
2.6417-2.68970.37851460.29982415X-RAY DIFFRACTION100
2.6897-2.74140.28051420.27812384X-RAY DIFFRACTION99
2.7414-2.79740.28451420.27332347X-RAY DIFFRACTION99
2.7974-2.85820.30321450.25842449X-RAY DIFFRACTION100
2.8582-2.92460.30751430.24682391X-RAY DIFFRACTION99
2.9246-2.99770.28811460.24032427X-RAY DIFFRACTION100
2.9977-3.07880.32241390.23942363X-RAY DIFFRACTION99
3.0788-3.16930.29381440.24852424X-RAY DIFFRACTION99
3.1693-3.27160.30641370.222354X-RAY DIFFRACTION99
3.2716-3.38840.29641390.21132405X-RAY DIFFRACTION99
3.3884-3.5240.23931390.20122358X-RAY DIFFRACTION98
3.524-3.68430.24681400.18132360X-RAY DIFFRACTION98
3.6843-3.87840.24521370.17692361X-RAY DIFFRACTION97
3.8784-4.12110.25641340.16442324X-RAY DIFFRACTION97
4.1211-4.43890.19691390.15192390X-RAY DIFFRACTION97
4.4389-4.88480.16161390.14032292X-RAY DIFFRACTION97
4.8848-5.58990.19751450.15082333X-RAY DIFFRACTION96
5.5899-7.0360.22711430.17422331X-RAY DIFFRACTION97
7.036-39.00990.17811420.15332343X-RAY DIFFRACTION97
Refinement TLS params.Method: refined / Origin x: 28.995 Å / Origin y: 55.231 Å / Origin z: 38.5428 Å
111213212223313233
T0.371 Å2-0.0529 Å2-0.0141 Å2-0.3825 Å20.0071 Å2--0.3007 Å2
L1.5106 °21.4841 °20.2467 °2-1.9455 °20.0109 °2--0.0129 °2
S0.035 Å °0.0046 Å °0.0023 Å °-0.0278 Å °-0.0026 Å °0.046 Å °0.0582 Å °-0.0198 Å °-0.0001 Å °
Refinement TLS groupSelection details: ALL

+
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