[English] 日本語
Yorodumi
- PDB-1pyy: Double mutant PBP2x T338A/M339F from Streptococcus pneumoniae str... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1pyy
TitleDouble mutant PBP2x T338A/M339F from Streptococcus pneumoniae strain R6 at 2.4 A resolution
ComponentsPenicillin-binding protein 2X
KeywordsTRANSPEPTIDASE / PENICILLIN-BINDING PROTEIN / ANTIBIOTIC RESISTANCE / PEPTIDOGLYCAN SYNTHESIS / CELL WALL / TRANSMEMBRANE
Function / homology
Function and homology information


penicillin binding / peptidoglycan biosynthetic process / cell wall organization / regulation of cell shape / cell division / response to antibiotic / plasma membrane
Similarity search - Function
: / PASTA domain / PASTA domain / PASTA domain profile. / PASTA / Penicillin-binding protein 2a (Domain 2) / Penicillin-binding protein 2a (Domain 2) / Penicillin-binding protein, dimerisation domain / Penicillin-binding Protein dimerisation domain / Penicillin-binding protein, dimerisation domain superfamily ...: / PASTA domain / PASTA domain / PASTA domain profile. / PASTA / Penicillin-binding protein 2a (Domain 2) / Penicillin-binding protein 2a (Domain 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 / DD-peptidase/beta-lactamase superfamily / Beta-lactamase/transpeptidase-like / Alpha-Beta Complex / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
octanoyl-sucrose, esterificated at fructose C6 / Penicillin-binding protein 2X
Similarity search - Component
Biological speciesStreptococcus pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.42 Å
AuthorsChesnel, L. / Pernot, L. / Lemaire, D. / Champelovier, D. / Croize, J. / Dideberg, O. / Vernet, T. / Zapun, A.
Citation
Journal: J.Biol.Chem. / Year: 2003
Title: The Structural Modifications Induced by the M339F Substitution in PBP2x from Streptococcus pneumoniae Further Decreases the Susceptibility to beta-Lactams of Resistant Strains
Authors: Chesnel, L. / Pernot, L. / Lemaire, D. / Champelovier, D. / Croize, J. / Dideberg, O. / Vernet, T. / Zapun, A.
#1: Journal: J.Biol.Chem. / Year: 2001
Title: CRYSTAL STRUCTURE OF PBP2X FROM A HIGHLY PENICILLIN-RESISTANT STREPTOCOCCUS PNEUMONIAE CLINICAL ISOLATE
Authors: DESSEN, A. / MOUZ, N. / Gordon, E. / HOPKINS, J. / DIDEBERG, O.
#2: Journal: J.Mol.Biol. / Year: 2000
Title: THE CRYSTAL STRUCTURE OF THE PENICILLIN BINDING PROTEIN 2X FROM STREPTOCOCCUS PNEUMONIAE AND ITS ACYL-ENZYME FORM: IMPLICATION IN DRUG RESISTANCE
Authors: GORDON, E. / MOUZ, N. / DUEE, E. / DIDEBERG, O.
#3: Journal: Nat.Struct.Biol. / Year: 1996
Title: X-RAY STRUCTURE OF STREPTOCOCCUS PNEUMONIAE PBP2X, A PRIMARY PENICILLIN TARGET ENZYME
Authors: PARES, S. / MOUZ, N. / PETILLOT, Y. / HAKENBECK, R. / DIDEBERG, O.
History
DepositionJul 9, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 30, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / entity_name_com / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_molecule_features / pdbx_nonpoly_scheme / struct_conn / struct_site / struct_site_gen
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_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.pdbx_synonyms / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.src_method / _entity.type
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Oct 27, 2021Group: Database references / Structure summary / Category: chem_comp / database_2 / struct_ref_seq_dif
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 2.2Aug 16, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Remark 600HETEROGEN The octanoyl chain is bound to the fructose group instead of the glucose group.

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Penicillin-binding protein 2X
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,4774
Polymers76,7941
Non-polymers6833
Water4,342241
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)128.224, 64.746, 146.974
Angle α, β, γ (deg.)90.00, 118.89, 90.00
Int Tables number5
Space group name H-MC121

-
Components

#1: Protein Penicillin-binding protein 2X / PBP-2X / PBP2X


Mass: 76793.922 Da / Num. of mol.: 1 / Mutation: T338A, M339F
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus pneumoniae (bacteria) / Strain: R6 / Gene: PBPX / Plasmid: PGEX / Production host: Escherichia coli (E. coli) / Strain (production host): MC1061 / References: UniProt: P59676
#2: Polysaccharide 6-O-octanoyl-beta-D-fructofuranose-(2-1)-alpha-D-glucopyranose / octanoyl-sucrose / esterificated at fructose C6


Type: oligosaccharide, Oligosaccharide / Class: Substrate analog / Mass: 468.493 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: oligosaccharide with reducing-end-to-reducing-end glycosidic bond
References: octanoyl-sucrose, esterificated at fructose C6
DescriptorTypeProgram
WURCS=2.0/2,2,1/[ha122h-2b_2-5_6*OCCCCCCCC/3=O][a2122h-1a_1-5]/1-2/a2-b1WURCSPDB2Glycan 1.1.0
[][b-D-Fruf]{[(2+1)][a-D-Glcp]{}}LINUCSPDB-CARE
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 241 / 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: 3.5 Å3/Da / Density % sol: 64.4 %
Crystal growTemperature: 281 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 12% PEG 6000, 100 mM sodium acetate, 200 mM ammonium sulfate, glycyl-glycyl-glycine, n-octanoylsucrose, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 281K
Crystal grow
*PLUS
pH: 8 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
150 mMTris1droppH8.0
2100 mM1dropNaCl
31 mMEDTA1drop
412 mg/mlprotein1drop
514 %PEG60001reservoir
6100 mMsodium acetate1reservoirpH4.6
7200 mMammonium sulfate1reservoir

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.99987 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Dec 18, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99987 Å / Relative weight: 1
ReflectionResolution: 2.42→31 Å / Num. obs: 40275 / % possible obs: 99.6 % / Observed criterion σ(I): 2 / Redundancy: 7.4 % / Biso Wilson estimate: 37.4 Å2 / Rmerge(I) obs: 0.048 / Net I/σ(I): 29.7
Reflection shellResolution: 2.42→2.55 Å / Redundancy: 6 % / Rmerge(I) obs: 0.198 / Mean I/σ(I) obs: 3.5 / % possible all: 98.2
Reflection
*PLUS
Num. measured all: 299369
Reflection shell
*PLUS
% possible obs: 98.2 %

-
Processing

Software
NameVersionClassification
CNS1.1refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1QME

1qme


Resolution: 2.42→30.69 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 1610393.46 / Data cutoff high rms absF: 1610393.46 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.244 2014 5 %RANDOM
Rwork0.218 ---
all0.244 ---
obs0.218 40275 99.6 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 43.2897 Å2 / ksol: 0.32268 e/Å3
Displacement parametersBiso mean: 52.4 Å2
Baniso -1Baniso -2Baniso -3
1-10.49 Å20 Å28.58 Å2
2---2.04 Å20 Å2
3----8.45 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.36 Å0.31 Å
Luzzati d res low-5 Å
Luzzati sigma a0.33 Å0.27 Å
Refinement stepCycle: LAST / Resolution: 2.42→30.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4642 0 45 241 4928
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d23.4
X-RAY DIFFRACTIONc_improper_angle_d0.81
X-RAY DIFFRACTIONc_mcbond_it2.772
X-RAY DIFFRACTIONc_mcangle_it4.162.5
X-RAY DIFFRACTIONc_scbond_it4.012.5
X-RAY DIFFRACTIONc_scangle_it5.383
LS refinement shellResolution: 2.42→2.55 Å / Rfactor Rfree error: 0.017 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.288 277 4.9 %
Rwork0.283 5327 -
obs--81.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2ION.PARAMION.TOP
X-RAY DIFFRACTION3WATER_REP.PARAMWATER_REP.TOP
X-RAY DIFFRACTION4OSUCROSE.PARAMOSUCROSE.TOP
X-RAY DIFFRACTION5MPD_CNS.PARAMMPD_CNS.TOP
Refinement
*PLUS
Lowest resolution: 31 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.43
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg23.4
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.81

+
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