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- PDB-6syn: Crystal structure of Y. pestis penicillin-binding protein 3 -

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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 / serine-type D-Ala-D-Ala carboxypeptidase activity / division septum assembly / FtsZ-dependent cytokinesis / penicillin binding / peptidoglycan biosynthetic process / cell wall organization / regulation of cell shape / 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 / Peptidoglycan D,D-transpeptidase FtsI / 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
Revision 1.2Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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

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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


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


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

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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: 2.04 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)

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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

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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 %

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