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

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Basic information

Entry
Database: PDB / ID: 3zga
TitleCrystal Structure of Penicillin-Binding Protein 4 from Listeria monocytogenes in the Carbenicillin bound form
Components(PENICILLIN-BINDING PROTEIN 4) x 2
KeywordsPENICILLIN-BINDING PROTEIN
Function / homology
Function and homology information


peptidoglycan glycosyltransferase activity / serine-type D-Ala-D-Ala carboxypeptidase activity / penicillin binding / peptidoglycan biosynthetic process / cell wall organization / regulation of cell shape / outer membrane-bounded periplasmic space / proteolysis / membrane
Similarity search - Function
Rhinovirus 14, subunit 4 - #110 / Rhinovirus 14, subunit 4 / Glycosyl transferase, family 51 / Penicillin binding protein transglycosylase domain / : / Transglycosylase / Other non-globular / Penicillin-binding protein, transpeptidase / Penicillin binding protein transpeptidase domain / Beta-lactamase ...Rhinovirus 14, subunit 4 - #110 / Rhinovirus 14, subunit 4 / Glycosyl transferase, family 51 / Penicillin binding protein transglycosylase domain / : / Transglycosylase / Other non-globular / Penicillin-binding protein, transpeptidase / Penicillin binding protein transpeptidase domain / Beta-lactamase / DD-peptidase/beta-lactamase superfamily / Special / Beta-lactamase/transpeptidase-like / Lysozyme-like domain superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-CB9 / Lmo2229 protein
Similarity search - Component
Biological speciesLISTERIA MONOCYTOGENES (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.005 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
Revision 1.3Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)63,8066
Polymers63,1492
Non-polymers6574
Water2,054114
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4320 Å2
ΔGint-25.8 kcal/mol
Surface area20760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.813, 127.777, 54.661
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 4 / 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
Details: CARBENICILLIN BOUND TO SER394, 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
#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: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 18.015 Da / Num. of mol.: 114 / Source method: isolated from a natural source / Formula: H2O
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: 1.64 Å3/Da / Density % sol: 24.97 % / Description: NONE
Crystal growpH: 7
Details: 20% POLYETHYLENE GLYCOL 3350, 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→30 Å / Num. obs: 39480 / % possible obs: 97.2 % / Observed criterion σ(I): 24.9 / Redundancy: 4.8 % / Biso Wilson estimate: 30.31 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 24.9
Reflection shellResolution: 2→2.08 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.3 / Mean I/σ(I) obs: 4.1 / % possible all: 85.2

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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: 2.005→26.726 Å / SU ML: 0.24 / σ(F): 1.5 / Phase error: 22.33 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2256 2000 5.1 %
Rwork0.185 --
obs0.187 39477 97.17 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 45.5 Å2
Refinement stepCycle: LAST / Resolution: 2.005→26.726 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3790 0 44 114 3948
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083904
X-RAY DIFFRACTIONf_angle_d1.1075294
X-RAY DIFFRACTIONf_dihedral_angle_d17.1441447
X-RAY DIFFRACTIONf_chiral_restr0.071588
X-RAY DIFFRACTIONf_plane_restr0.005687
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0049-2.05510.33191210.28422270X-RAY DIFFRACTION84
2.0551-2.11060.29531290.27062417X-RAY DIFFRACTION89
2.1106-2.17270.28831370.25122576X-RAY DIFFRACTION95
2.1727-2.24280.27181430.22472667X-RAY DIFFRACTION98
2.2428-2.32290.2261420.22212674X-RAY DIFFRACTION99
2.3229-2.41580.24691440.21162700X-RAY DIFFRACTION99
2.4158-2.52570.24841450.20582699X-RAY DIFFRACTION99
2.5257-2.65880.26391460.19752732X-RAY DIFFRACTION99
2.6588-2.82520.26241450.19352717X-RAY DIFFRACTION99
2.8252-3.0430.25991460.20062744X-RAY DIFFRACTION99
3.043-3.34870.23131470.19522745X-RAY DIFFRACTION100
3.3487-3.83210.2281480.17062777X-RAY DIFFRACTION100
3.8321-4.82340.18111500.13772821X-RAY DIFFRACTION100
4.8234-26.72830.17391570.1612938X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 11.364 Å / Origin y: -22.0677 Å / Origin z: -11.0694 Å
111213212223313233
T0.194 Å20.0004 Å2-0.0493 Å2-0.3119 Å2-0.0257 Å2--0.214 Å2
L1.101 °20.409 °2-0.2838 °2-1.4672 °2-1.0092 °2--1.8659 °2
S0.0303 Å °-0.0271 Å °0.1697 Å °-0.0194 Å °-0.0056 Å °0.1006 Å °-0.1339 Å °-0.0085 Å °-0.0295 Å °
Refinement TLS groupSelection details: ALL

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