[English] 日本語
Yorodumi
- PDB-5oau: Penicillin-Binding Protein 2X (PBP2X) from Streptococcus pneumoniae -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5oau
TitlePenicillin-Binding Protein 2X (PBP2X) from Streptococcus pneumoniae
ComponentsPenicillin-binding protein 2X
KeywordsANTIBIOTIC / Penicillin / b-lactam / cell-wall / transpeptidase
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, dimerisation domain / Penicillin-binding Protein dimerisation domain / Penicillin-binding protein, dimerisation domain superfamily / : / Penicillin-binding protein, transpeptidase ...: / PASTA domain / PASTA domain / PASTA domain profile. / PASTA / 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 / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
PASTA domain-containing protein / Penicillin-binding protein 2X
Similarity search - Component
Biological speciesStreptococcus pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.67 Å
AuthorsBernardo-Garcia, N. / Hermoso, J.A.
CitationJournal: ACS Chem. Biol. / Year: 2018
Title: Allostery, Recognition of Nascent Peptidoglycan, and Cross-linking of the Cell Wall by the Essential Penicillin-Binding Protein 2x of Streptococcus pneumoniae.
Authors: Bernardo-Garcia, N. / Mahasenan, K.V. / Batuecas, M.T. / Lee, M. / Hesek, D. / Petrackova, D. / Doubravova, L. / Branny, P. / Mobashery, S. / Hermoso, J.A.
History
DepositionJun 23, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 30, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2024Group: 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: Penicillin-binding protein 2X


Theoretical massNumber of molelcules
Total (without water)76,8081
Polymers76,8081
Non-polymers00
Water4,125229
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 area30700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)100.260, 100.260, 189.810
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

-
Components

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


Mass: 76807.969 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus pneumoniae (bacteria) / Gene: pbpX, spr0304 / Production host: Escherichia coli (E. coli) / References: UniProt: P59676, UniProt: A0A0E8T757*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 229 / 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: 3.57 Å3/Da / Density % sol: 65.51 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 4.5 / Details: 2.3-3.0 M NaCl, 0.1 M sodium acetate

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.97947 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 17, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97947 Å / Relative weight: 1
ReflectionResolution: 2.67→34.78 Å / Num. obs: 31872 / % possible obs: 99.3 % / Redundancy: 3.5 % / Rmerge(I) obs: 0.1 / Rpim(I) all: 0.09 / Net I/σ(I): 7.5
Reflection shellResolution: 2.67→2.8 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.57 / Mean I/σ(I) obs: 1.7 / Rpim(I) all: 0.48 / % possible all: 99.1

-
Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
XDSdata scaling
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1k25

1k25


Resolution: 2.67→34.78 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.912 / SU B: 5.889 / SU ML: 0.134 / Cross valid method: THROUGHOUT / ESU R: 0.36 / ESU R Free: 0.256 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22531 1506 4.7 %RANDOM
Rwork0.17345 ---
obs0.17588 30573 99.88 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 62.804 Å2
Baniso -1Baniso -2Baniso -3
1--0.05 Å2-0.03 Å20 Å2
2---0.05 Å20 Å2
3---0.17 Å2
Refinement stepCycle: 1 / Resolution: 2.67→34.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5131 0 0 229 5360
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.025219
X-RAY DIFFRACTIONr_bond_other_d0.0020.024760
X-RAY DIFFRACTIONr_angle_refined_deg1.7421.9577069
X-RAY DIFFRACTIONr_angle_other_deg1.056311119
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.285664
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.58725.801231
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.94315907
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.9031519
X-RAY DIFFRACTIONr_chiral_restr0.1030.2805
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0215821
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02970
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it5.2596.2062665
X-RAY DIFFRACTIONr_mcbond_other5.2596.2042664
X-RAY DIFFRACTIONr_mcangle_it7.8719.33326
X-RAY DIFFRACTIONr_mcangle_other7.879.3023327
X-RAY DIFFRACTIONr_scbond_it5.4646.6942554
X-RAY DIFFRACTIONr_scbond_other5.4646.6912552
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other7.9539.8563743
X-RAY DIFFRACTIONr_long_range_B_refined12.24972.8285625
X-RAY DIFFRACTIONr_long_range_B_other12.24772.8165618
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.67→2.739 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.158 95 -
Rwork0.098 2256 -
obs--99.83 %

+
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