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- PDB-7ono: Crystal structure of PBP3 transpeptidase domain from E. coli -

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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 / serine-type D-Ala-D-Ala carboxypeptidase activity / division septum assembly / FtsZ-dependent cytokinesis / cell division site / penicillin binding / peptidoglycan biosynthetic process / cell wall organization ...divisome complex / peptidoglycan glycosyltransferase activity / serine-type D-Ala-D-Ala carboxypeptidase / serine-type D-Ala-D-Ala carboxypeptidase activity / division septum assembly / FtsZ-dependent cytokinesis / cell division site / penicillin binding / peptidoglycan biosynthetic process / cell wall organization / regulation of cell shape / response to xenobiotic stimulus / cell division / proteolysis / plasma membrane
Similarity search - Function
Penicillin-binding protein 2a (Domain 2) / Penicillin-binding protein 2a (Domain 2) / 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 ...Penicillin-binding protein 2a (Domain 2) / Penicillin-binding protein 2a (Domain 2) / 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 / Alpha-Beta Complex / Alpha Beta
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
Revision 1.2Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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

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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) (bacteria)
Strain: K12 / Gene: ftsI, pbpB, b0084, JW0082 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: P0AD68, serine-type D-Ala-D-Ala carboxypeptidase
#2: Chemical ChemComp-TMO / trimethylamine oxide


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


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

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Experimental details

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Experiment

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

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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

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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

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Phasing

PhasingMethod: molecular replacement

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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

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

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)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

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