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- PDB-8gpw: Structure of Penicillin-binding protein 3 (PBP3) from Klebsiella ... -

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Basic information

Entry
Database: PDB / ID: 8gpw
TitleStructure of Penicillin-binding protein 3 (PBP3) from Klebsiella pneumoniae with ligand 18G
ComponentsPeptidoglycan D,D-transpeptidase FtsI
KeywordsTRANSFERASE / penicillin binding / cell wall organization or biogenesis / plasma membrane
Function / homology
Function and homology information


peptidoglycan glycosyltransferase activity / serine-type D-Ala-D-Ala carboxypeptidase / FtsZ-dependent cytokinesis / division septum assembly / serine-type D-Ala-D-Ala carboxypeptidase activity / plasma membrane => GO:0005886 / penicillin binding / peptidoglycan biosynthetic process / cell wall organization / regulation of cell shape / proteolysis
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
Chem-JXJ / Peptidoglycan D,D-transpeptidase FtsI
Similarity search - Component
Biological speciesKlebsiella pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.06 Å
AuthorsSong, D.Q. / Li, Y.H.
Funding support United Kingdom, 2items
OrganizationGrant numberCountry
CAMS Innovation Fund for Medical Sciences (CIFMS)2021-I2M-1-070 United Kingdom
CAMS Innovation Fund for Medical Sciences (CIFMS)2021-I2M-1-030 United Kingdom
CitationJournal: To Be Published
Title: Structure of Penicillin-binding protein 3 (PBP3) from Klebsiella pneumoniae with ligand 18G at 2.06 Angstroms resolution
Authors: Song, D.Q. / Li, Y.H.
History
DepositionAug 27, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 2, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: 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

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Assembly

Deposited unit
A: Peptidoglycan D,D-transpeptidase FtsI
B: Peptidoglycan D,D-transpeptidase FtsI
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,1824
Polymers87,2512
Non-polymers9312
Water2,954164
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1850 Å2
ΔGint3 kcal/mol
Surface area30520 Å2
Unit cell
Length a, b, c (Å)95.400, 103.660, 80.250
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

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Components

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


Mass: 43625.645 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella pneumoniae (bacteria) / Gene: ftsI, ETE64_07005 / Production host: Escherichia coli (E. coli)
References: UniProt: A0A483LPP8, serine-type D-Ala-D-Ala carboxypeptidase
#2: Chemical ChemComp-JXJ / 1-[(~{Z})-[1-(2-azanyl-1,3-thiazol-4-yl)-2-[[(2~{S})-3-methyl-1-oxidanylidene-3-(sulfooxyamino)butan-2-yl]amino]-2-oxidanylidene-ethylidene]amino]oxycyclopropane-1-carboxylic acid


Mass: 465.459 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H19N5O9S2 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 164 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.26 Å3/Da / Density % sol: 45.51 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 28% PEG 4000, 0.1 M Tris pH 8.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.97915 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 2, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 2.06→43.54 Å / Num. obs: 49615 / % possible obs: 99.3 % / Redundancy: 7 % / Biso Wilson estimate: 38.67 Å2 / Rmerge(I) obs: 0.146 / Net I/σ(I): 7.7
Reflection shellResolution: 2.06→2.11 Å / Redundancy: 5.1 % / Rmerge(I) obs: 1.319 / Num. unique obs: 3409 / % possible all: 92.9

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
xia2data scaling
PDB_EXTRACT3.27data extraction
xia2data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4BJP
Resolution: 2.06→43.54 Å / SU ML: 0.27 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 26.38 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2359 1999 4.03 %
Rwork0.1996 47554 -
obs0.201 49553 99.28 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 124.5 Å2 / Biso mean: 48.1138 Å2 / Biso min: 23.31 Å2
Refinement stepCycle: final / Resolution: 2.06→43.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5985 0 92 164 6241
Biso mean--63.75 43.67 -
Num. residues----794
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.06-2.110.34671370.31893132326993
2.11-2.170.36541470.2773283343098
2.17-2.230.34511330.244533683501100
2.23-2.30.27811520.235333833535100
2.3-2.390.28571320.218134073539100
2.39-2.480.28481410.211133543495100
2.48-2.60.31461460.214933963542100
2.6-2.730.26941420.23233933535100
2.73-2.90.30231410.226434033544100
2.9-3.130.25231400.211634433583100
3.13-3.440.27391380.213834233561100
3.44-3.940.21611500.187734393589100
3.94-4.960.1811490.159234903639100
4.96-43.540.1761510.177436403791100
Refinement TLS params.Method: refined / Origin x: 14.8957 Å / Origin y: 13.4178 Å / Origin z: 14.7028 Å
111213212223313233
T0.2453 Å2-0.0252 Å20.0145 Å2-0.2531 Å2-0.034 Å2--0.3299 Å2
L0.5918 °2-0.1757 °20.0917 °2-0.6413 °2-0.6003 °2--1.8192 °2
S-0.0723 Å °-0.1074 Å °0.0459 Å °0.0489 Å °-0.0249 Å °-0.1085 Å °-0.0372 Å °0.1072 Å °0.1133 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA70 - 570
2X-RAY DIFFRACTION1allB70 - 570
3X-RAY DIFFRACTION1allS1 - 256
4X-RAY DIFFRACTION1allC2 - 3

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