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- PDB-3zg8: Crystal Structure of Penicillin Binding Protein 4 from Listeria m... -

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Basic information

Entry
Database: PDB / ID: 3zg8
TitleCrystal Structure of Penicillin Binding Protein 4 from Listeria monocytogenes in the Ampicillin bound form
Components
  • PENICILLIN-BINDING PROTEIN 4
  • PENICILLIN-BINDING PROTEINPenicillin-binding proteins
KeywordsPENICILLIN-BINDING PROTEIN
Function / homology
Function and homology information


peptidoglycan glycosyltransferase / peptidoglycan glycosyltransferase activity / serine-type D-Ala-D-Ala carboxypeptidase activity / penicillin binding / peptidoglycan biosynthetic process / response to antibiotic / proteolysis / membrane
Similarity search - Function
Glycosyl transferase, family 51 / Penicillin binding protein transglycosylase domain / Transglycosylase / Penicillin-binding protein, transpeptidase / Penicillin binding protein transpeptidase domain / Beta-lactamase / DD-peptidase/beta-lactamase superfamily / Beta-lactamase/transpeptidase-like / Lysozyme-like domain superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-AIX / peptidoglycan glycosyltransferase
Similarity search - Component
Biological speciesLISTERIA MONOCYTOGENES (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.094 Å
AuthorsJeong, J.H. / Kim, Y.G.
CitationJournal: Antimicrob.Agents Chemother. / Year: 2013
Title: Crystal Structures of Bifunctional Penicillin-Binding Protein 4 from Listeria Monocytogenes.
Authors: Jeong, J. / Kim, Y. / Rojviriya, C. / Ha, S. / Kang, B.S. / Kim, Y.
History
DepositionDec 17, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 29, 2013Provider: repository / Type: Initial release
Revision 1.1Jul 31, 2013Group: Database references
Revision 1.2Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PENICILLIN-BINDING PROTEIN
B: PENICILLIN-BINDING PROTEIN 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,7776
Polymers63,1492
Non-polymers6284
Water2,180121
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4150 Å2
ΔGint-24.8 kcal/mol
Surface area20720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.746, 128.294, 54.732
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein/peptide PENICILLIN-BINDING PROTEIN / Penicillin-binding proteins / LMO2229 PROTEIN


Mass: 5049.557 Da / Num. of mol.: 1 / Fragment: RESIDUES 73-119
Source method: isolated from a genetically manipulated source
Details: PROTEOLYSIS FROM 120-177 / Source: (gene. exp.) LISTERIA MONOCYTOGENES (bacteria) / Plasmid: PPROEXHTA / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): RIL / References: UniProt: Q8Y547
#2: Protein PENICILLIN-BINDING PROTEIN 4 / LMO2229 PROTEIN


Mass: 58099.547 Da / Num. of mol.: 1 / Fragment: RESIDUES 178-714
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) LISTERIA MONOCYTOGENES (bacteria) / Plasmid: PPROEXHTA / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): RIL / References: UniProt: Q8Y547
#3: Chemical ChemComp-AIX / (2R,4S)-2-[(1R)-1-{[(2R)-2-amino-2-phenylacetyl]amino}-2-oxoethyl]-5,5-dimethyl-1,3-thiazolidine-4-carboxylic acid / AMPICILLIN (open form)


Mass: 351.421 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H21N3O4S
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 121 / Source method: isolated from a natural source / Formula: H2O

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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: 1.91 Å3/Da / Density % sol: 35.75 % / Description: NONE
Crystal growpH: 7
Details: 20% POLYETHYLENE GLYCOL 3,350 0.1M AMMONIUM TARTRATE (PH 7.0)

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Data collection

DiffractionMean temperature: 295 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 4A / Wavelength: 0.9795
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 20, 2010 / Details: MIRRORS
RadiationMonochromator: DOUBLE CRYSTAL MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.1→30 Å / Num. obs: 35362 / % possible obs: 98.5 % / Observed criterion σ(I): 0 / Redundancy: 5.5 % / Biso Wilson estimate: 32.48 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 27.3
Reflection shellResolution: 2.1→2.18 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.32 / Mean I/σ(I) obs: 4.5 / % possible all: 88.3

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3ZG7

3zg7


Resolution: 2.094→29.698 Å / SU ML: 0.27 / σ(F): 1.48 / Phase error: 22.87 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2334 2000 5.7 %
Rwork0.192 --
obs0.1943 35358 98.5 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 25.8 Å2
Refinement stepCycle: LAST / Resolution: 2.094→29.698 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3773 0 42 121 3936
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.013884
X-RAY DIFFRACTIONf_angle_d1.085268
X-RAY DIFFRACTIONf_dihedral_angle_d13.7381406
X-RAY DIFFRACTIONf_chiral_restr0.072590
X-RAY DIFFRACTIONf_plane_restr0.005682
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0944-2.14680.30411220.26532048X-RAY DIFFRACTION86
2.1468-2.20480.28981370.24332274X-RAY DIFFRACTION96
2.2048-2.26970.28611410.23782346X-RAY DIFFRACTION99
2.2697-2.34290.27361420.22762382X-RAY DIFFRACTION99
2.3429-2.42660.28211420.22212361X-RAY DIFFRACTION100
2.4266-2.52370.28111450.21562410X-RAY DIFFRACTION100
2.5237-2.63850.26621420.2092385X-RAY DIFFRACTION100
2.6385-2.77750.27131440.20962395X-RAY DIFFRACTION100
2.7775-2.95140.26251440.21872403X-RAY DIFFRACTION100
2.9514-3.1790.25731450.21272417X-RAY DIFFRACTION100
3.179-3.49850.23851450.19982422X-RAY DIFFRACTION100
3.4985-4.00370.20661480.17662454X-RAY DIFFRACTION100
4.0037-5.04020.18911480.14512474X-RAY DIFFRACTION100
5.0402-29.70120.19031550.16762587X-RAY DIFFRACTION100

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