[English] 日本語
Yorodumi
- PDB-6syn: Crystal structure of Y. pestis penicillin-binding protein 3 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6syn
TitleCrystal structure of Y. pestis penicillin-binding protein 3
ComponentsPeptidoglycan D,D-transpeptidase FtsI
KeywordsCYTOSOLIC PROTEIN / Class B PBP / Yersinia pestis / HMM transpeptidase / periplasmic protein
Function / homology
Function and homology information


peptidoglycan glycosyltransferase activity / serine-type D-Ala-D-Ala carboxypeptidase / FtsZ-dependent cytokinesis / serine-type D-Ala-D-Ala carboxypeptidase activity / division septum assembly / plasma membrane => GO:0005886 / penicillin binding / peptidoglycan biosynthetic process / cell wall organization / regulation of cell shape ...peptidoglycan glycosyltransferase activity / serine-type D-Ala-D-Ala carboxypeptidase / FtsZ-dependent cytokinesis / serine-type D-Ala-D-Ala carboxypeptidase activity / division septum assembly / plasma membrane => GO:0005886 / penicillin binding / peptidoglycan biosynthetic process / cell wall organization / regulation of cell shape / membrane => GO:0016020 / proteolysis / plasma membrane
Similarity search - Function
Peptidoglycan D,D-transpeptidase FtsI / 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
ACETATE ION / Chem-CB9 / Penicillin-binding protein 3 / Peptidoglycan D,D-transpeptidase FtsI
Similarity search - Component
Biological speciesYersinia pestis (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.63 Å
AuthorsPankov, G. / Hunter, W.N. / Dawson, A.
CitationJournal: To Be Published
Title: The structure of penicillin-binding protein 3 from Yersinia pestis
Authors: Pankov, G.
History
DepositionSep 30, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 14, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 24, 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: Peptidoglycan D,D-transpeptidase FtsI
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,1454
Polymers57,6471
Non-polymers4993
Water2,594144
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area350 Å2
ΔGint-1 kcal/mol
Surface area20000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)40.860, 104.950, 110.420
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP22121

-
Components

#1: Protein Peptidoglycan D,D-transpeptidase FtsI / Penicillin-binding protein 3 / PBP-3


Mass: 57646.836 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Yersinia pestis (bacteria) / Gene: ftsI, YPO0549 / Production host: Escherichia coli (E. coli)
References: UniProt: Q0WJB8, UniProt: A0A3N4B5A3*PLUS, serine-type D-Ala-D-Ala carboxypeptidase
#2: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical ChemComp-CB9 / (2R,4S)-2-[(1R)-1-{[(2S)-2-carboxy-2-phenylacetyl]amino}-2-oxoethyl]-5,5-dimethyl-1,3-thiazolidine-4-carboxylic acid / Bound form of Carbenicillin


Mass: 380.416 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H20N2O6S
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 144 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.04 Å3/Da / Density % sol: 40 % / Description: rectangular prisms
Crystal growTemperature: 296 K / Method: vapor diffusion, sitting drop
Details: 0.2 uL of protein (in 20 mM Tris-HCl pH 7.5 150 mM NaCl and 2 mM carbenicillin) at 6.7 mg/ml and 0.2 uL of precipitant (0.2 M magnesium acetate, 0.1 M sodium cacodylate pH 6.5 and 20% PEG 8000)

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54178 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: Jan 16, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 2.63→36 Å / Num. obs: 14613 / % possible obs: 98.7 % / Redundancy: 3.9 % / Biso Wilson estimate: 8.1 Å2 / CC1/2: 0.971 / Rmerge(I) obs: 0.122 / Rpim(I) all: 0.097 / Rrim(I) all: 0.153 / Net I/σ(I): 7.8
Reflection shellResolution: 2.63→2.74 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.234 / Mean I/σ(I) obs: 3.9 / Num. unique obs: 1663 / CC1/2: 0.652 / Rpim(I) all: 0.203 / Rrim(I) all: 0.312 / % possible all: 93.8

-
Processing

Software
NameVersionClassification
Aimlessdata scaling
REFMAC5.8.0238refinement
PDB_EXTRACT3.25data extraction
MOSFLMdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4BJP

4bjp


Resolution: 2.63→36 Å / Cor.coef. Fo:Fc: 0.895 / Cor.coef. Fo:Fc free: 0.819 / SU B: 13.841 / SU ML: 0.288 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.382
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.273 752 5.2 %RANDOM
Rwork0.2083 ---
obs0.2118 13830 98.48 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 62 Å2 / Biso mean: 15.899 Å2 / Biso min: 5 Å2
Baniso -1Baniso -2Baniso -3
1--0.37 Å20 Å20 Å2
2---0.46 Å20 Å2
3---0.83 Å2
Refinement stepCycle: final / Resolution: 2.63→36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3596 0 8 144 3748
Biso mean--26.63 11.01 -
Num. residues----471
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0030.0133679
X-RAY DIFFRACTIONr_bond_other_d0.0010.0173529
X-RAY DIFFRACTIONr_angle_refined_deg1.3881.6454997
X-RAY DIFFRACTIONr_angle_other_deg1.1131.5728144
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9515468
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.18320.862174
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.66515599
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.0341529
X-RAY DIFFRACTIONr_chiral_restr0.060.2483
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.024118
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02761
LS refinement shellResolution: 2.63→2.696 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.457 55 -
Rwork0.246 924 -
obs--90.82 %

+
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