[English] 日本語
Yorodumi
- PDB-7ono: Crystal structure of PBP3 transpeptidase domain from E. coli -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7ono
TitleCrystal structure of PBP3 transpeptidase domain from E. coli
ComponentsPeptidoglycan D,D-transpeptidase FtsI
KeywordsMEMBRANE PROTEIN / PBP3 / peptidoglycan synthesis / transpeptidase domain
Function / homology
Function and homology information


divisome complex / peptidoglycan glycosyltransferase activity / serine-type D-Ala-D-Ala carboxypeptidase / cell division site / FtsZ-dependent cytokinesis / division septum assembly / serine-type D-Ala-D-Ala carboxypeptidase activity / : / penicillin binding / peptidoglycan biosynthetic process ...divisome complex / peptidoglycan glycosyltransferase activity / serine-type D-Ala-D-Ala carboxypeptidase / cell division site / FtsZ-dependent cytokinesis / division septum assembly / serine-type D-Ala-D-Ala carboxypeptidase activity / : / penicillin binding / peptidoglycan biosynthetic process / cell wall organization / regulation of cell shape / response to xenobiotic stimulus / cell division / plasma membrane => GO:0005886 / 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
trimethylamine oxide / Peptidoglycan D,D-transpeptidase FtsI
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.3 Å
AuthorsFreischem, S. / Grimm, I. / Weiergraeber, O.H.
CitationJournal: Biomolecules / Year: 2021
Title: Interaction Mode of the Novel Monobactam AIC499 Targeting Penicillin Binding Protein 3 of Gram-Negative Bacteria.
Authors: Freischem, S. / Grimm, I. / Lopez-Perez, A. / Willbold, D. / Klenke, B. / Vuong, C. / Dingley, A.J. / Weiergraber, O.H.
History
DepositionMay 25, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 4, 2021Provider: repository / Type: Initial release
Revision 1.1Sep 22, 2021Group: Data collection / Database references / Category: citation / database_2 / pdbx_database_proc
Item: _citation.journal_volume / _citation.pdbx_database_id_PubMed ..._citation.journal_volume / _citation.pdbx_database_id_PubMed / _citation.title / _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)43,7722
Polymers43,6971
Non-polymers751
Water28816
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 area17190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)109.280, 109.280, 143.229
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number180
Space group name H-MP6222
Space group name HallP622(x,y,z+1/3)
Symmetry operation#1: x,y,z
#2: x-y,x,z+1/3
#3: y,-x+y,z+2/3
#4: -y,x-y,z+2/3
#5: -x+y,-x,z+1/3
#6: x-y,-y,-z
#7: -x,-x+y,-z+1/3
#8: -x,-y,z
#9: y,x,-z+2/3
#10: -y,-x,-z+2/3
#11: -x+y,y,-z
#12: x,x-y,-z+1/3

-
Components

#1: Protein Peptidoglycan D,D-transpeptidase FtsI / Essential cell division protein FtsI / Murein transpeptidase / Penicillin-binding protein 3 / PBP-3 ...Essential cell division protein FtsI / Murein transpeptidase / Penicillin-binding protein 3 / PBP-3 / Peptidoglycan synthase FtsI


Mass: 43696.766 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (strain K12) (unknown)
Strain: K12 / Gene: ftsI, pbpB, b0084, JW0082 / Production host: Escherichia coli BL21(DE3) (unknown)
References: UniProt: P0AD68, serine-type D-Ala-D-Ala carboxypeptidase
#2: Chemical ChemComp-TMO / trimethylamine oxide / Trimethylamine N-oxide


Mass: 75.110 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H9NO
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 16 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.84 Å3/Da / Density % sol: 56.76 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 14.4 mg/ml PBP3, 0.1 M sodium cacodylate, 5% (w/v) PEG 8000, 20% (v/v) MPD, 0.2% (w/v) betaine, 0.2% (w/v) L-glutamic acid, 0.2% (w/v) L-proline, 0.2% (w/v) taurine, 0.2% (w/v) trimethlyamin ...Details: 14.4 mg/ml PBP3, 0.1 M sodium cacodylate, 5% (w/v) PEG 8000, 20% (v/v) MPD, 0.2% (w/v) betaine, 0.2% (w/v) L-glutamic acid, 0.2% (w/v) L-proline, 0.2% (w/v) taurine, 0.2% (w/v) trimethlyamin N-oxide, 0.02 M HEPES

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, DESY / Beamline: P11 / Wavelength: 1.0332 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: May 4, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 2.298→47.743 Å / Num. obs: 9457 / % possible obs: 93.9 % / Redundancy: 17.8 % / CC1/2: 0.999 / Rrim(I) all: 0.103 / Net I/σ(I): 20.7
Reflection shellResolution: 2.298→2.603 Å / Redundancy: 15.7 % / Mean I/σ(I) obs: 2.4 / Num. unique obs: 473 / CC1/2: 0.84 / Rrim(I) all: 1.456 / % possible all: 74.6

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassification
PHENIX1.19.1refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
PDB_EXTRACT3.27data extraction
STARANISOdata processing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4BJP
Resolution: 2.3→47.74 Å / SU ML: 0.2205 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 31.4743
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.282 469 4.96 %
Rwork0.2295 8987 -
obs0.2321 9456 40.84 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 66.52 Å2
Refinement stepCycle: LAST / Resolution: 2.3→47.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3001 0 5 16 3022
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00143096
X-RAY DIFFRACTIONf_angle_d0.40274212
X-RAY DIFFRACTIONf_chiral_restr0.0398484
X-RAY DIFFRACTIONf_plane_restr0.0037548
X-RAY DIFFRACTIONf_dihedral_angle_d8.26381130
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.630.4372340.3958498X-RAY DIFFRACTION7.07
2.63-3.310.3549980.33531803X-RAY DIFFRACTION24.95
3.31-47.740.27013370.21626686X-RAY DIFFRACTION87.95
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
10.08424663446850.2158875592940.6361694206213.980900604280.9532881821574.92297192940.408438812020.5798822852170.4076620851550.04435735730450.07447018531590.814274878202-0.0156596039199-2.04502242436-0.8277327163170.426870770390.2208398682720.05750770672961.24518797280.6174145437010.5951730755951.2346935370235.7737148927-16.1351710421
22.742336984090.4000069090730.4411851479322.112071734660.06274119622193.177194729790.6623442750850.1449936126020.175140151647-0.1657065340330.0002749351734150.3682338711610.0495622600828-0.673501942357-0.2160111656020.510126735430.301510400079-0.00783847108540.4502947379480.215280479990.32959087880615.373579620131.9919666953-11.9601062113
33.17094805901-1.103275986710.4011944237492.74220488449-1.140865873793.703189555330.1705718887950.0839362599093-0.516862115218-0.05648620150030.338615872867-0.05808937991561.182879699060.373845177198-0.4776555010160.6223052835670.10626045022-0.07995932672270.5904235935140.1191584681860.38558706977925.726755155219.49599251883.33356599815
42.824175121090.193910235576-0.03349904094160.8963127313420.02626064236552.140033541950.259094202075-1.06744210758-0.2880308185740.3640626228160.186293414330.1031333783040.6651545758520.117646532495-0.3082137657360.6227980734480.253774487375-0.08268428067050.694601130910.1451836664330.17315957620622.56501420726.07724490268.94016421082
54.15717665341-0.580024614530.443094591780.990330138840.5114498165324.252861582340.371629343568-0.700849405326-0.397440621092-0.0988878254413-0.190702491793-0.2616913728290.7694559098220.229739891426-0.2323084610210.5621278308370.276777730883-0.04761284233710.406102903329-0.02378992928010.34481572643729.863524409224.992571957-1.93318185747
62.78849496699-0.145018189815-0.7333141615692.209091217080.5290776083192.613299042250.2753927829210.141878746775-0.038230812366-0.7330646342010.297673483583-0.7078749402390.4651382688610.558600865033-0.3852667737360.5673481177990.334136948588-0.1019666251370.417011897907-0.01857236766040.43125013831531.187635233127.9438339021-11.7964404758
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A

IDRefine TLS-IDSelection detailsAuth seq-IDLabel seq-ID
11chain 'A' and (resid 69 through 201 )69 - 2011 - 61
22chain 'A' and (resid 202 through 278 )202 - 27862 - 117
33chain 'A' and (resid 279 through 348 )279 - 348118 - 187
44chain 'A' and (resid 349 through 460 )349 - 460188 - 299
55chain 'A' and (resid 461 through 533 )461 - 533300 - 372
66chain 'A' and (resid 534 through 569 )534 - 569373 - 406

+
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