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- PDB-5zqa: Crystal Structure of Penicillin-Binding Protein D2 from Listeria ... -

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Basic information

Entry
Database: PDB / ID: 5zqa
TitleCrystal Structure of Penicillin-Binding Protein D2 from Listeria monocytogenes in the apo form
ComponentsLmo2812 protein
KeywordsANTIBIOTIC / Listeria monocytogenes / hypothetical / penicillin-binding protein / LmPBPD2 / lmo2812
Function / homology
Function and homology information


serine-type D-Ala-D-Ala carboxypeptidase activity / peptidoglycan biosynthetic process / cell wall organization / regulation of cell shape / proteolysis / metal ion binding
Similarity search - Function
Peptidase S11, D-alanyl-D-alanine carboxypeptidase A, N-terminal / Peptidase S11, D-alanyl-D-alanine carboxypeptidase A / D-alanyl-D-alanine carboxypeptidase / Beta-lactamase/transpeptidase-like / Prokaryotic membrane lipoprotein lipid attachment site profile.
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / Lmo2812 protein
Similarity search - Component
Biological speciesListeria monocytogenes EGD-e (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 Å
AuthorsJeong, J.H. / Kim, Y.G.
Funding support Korea, Republic Of, 1items
OrganizationGrant numberCountry
National Research Foundation (Korea) Korea, Republic Of
CitationJournal: Antimicrob. Agents Chemother. / Year: 2018
Title: Crystal Structures of Penicillin-Binding Protein D2 from Listeria monocytogenes and Structural Basis for Antibiotic Specificity
Authors: Jeong, J.H. / Cha, H.J. / Kim, Y.G.
History
DepositionApr 18, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 25, 2018Provider: repository / Type: Initial release
Revision 1.1Aug 22, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_abbrev / _citation.journal_volume ..._citation.journal_abbrev / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Sep 12, 2018Group: Data collection / Database references / Category: citation / Item: _citation.journal_volume / _citation.title
Revision 1.3Nov 22, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Lmo2812 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,2715
Polymers30,0921
Non-polymers1794
Water2,954164
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area80 Å2
ΔGint-7 kcal/mol
Surface area10930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)37.669, 74.582, 74.955
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Lmo2812 protein


Mass: 30091.605 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Listeria monocytogenes EGD-e (bacteria)
Strain: EGD-e / Gene: lmo2812 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8Y3M3
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 164 / 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: 1.78 Å3/Da / Density % sol: 31.05 %
Crystal growTemperature: 295.15 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 0.2M Potassium chloride, 20%(w/v) Polyethylene glycol 3,350

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Data collection

DiffractionMean temperature: 200 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-1A / Wavelength: 1.1 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Jan 17, 2014
RadiationMonochromator: Cryo-cooled channel-cut Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 1.55→37.291 Å / Num. obs: 30734 / % possible obs: 97.83 % / Observed criterion σ(I): 0 / Redundancy: 5.8 % / Biso Wilson estimate: 12.61 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.08823 / Rrim(I) all: 0.09664 / Net I/σ(I): 22.6
Reflection shellResolution: 1.55→1.605 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.3248 / Num. unique obs: 2508 / CC1/2: 0.861 / % possible all: 81.09

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Processing

Software
NameVersionClassification
PHENIX1.9_1690refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3it9

3it9


Resolution: 1.55→37.291 Å / SU ML: 0.12 / Cross valid method: NONE / σ(F): 1.37 / Phase error: 16.66
RfactorNum. reflection% reflection
Rfree0.1885 1998 6.5 %
Rwork0.1645 --
obs0.166 30733 97.82 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.55→37.291 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1879 0 10 164 2053
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061909
X-RAY DIFFRACTIONf_angle_d1.012577
X-RAY DIFFRACTIONf_dihedral_angle_d12.225706
X-RAY DIFFRACTIONf_chiral_restr0.039305
X-RAY DIFFRACTIONf_plane_restr0.004330
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5501-1.58880.2151180.17251578X-RAY DIFFRACTION77
1.5888-1.63180.18971350.15181971X-RAY DIFFRACTION94
1.6318-1.67980.19481420.14872031X-RAY DIFFRACTION99
1.6798-1.7340.1991450.15772069X-RAY DIFFRACTION100
1.734-1.7960.2191450.15512065X-RAY DIFFRACTION100
1.796-1.86790.17811430.16192075X-RAY DIFFRACTION100
1.8679-1.95290.18621430.16052064X-RAY DIFFRACTION100
1.9529-2.05590.17661430.15712070X-RAY DIFFRACTION100
2.0559-2.18470.16521470.15412090X-RAY DIFFRACTION100
2.1847-2.35330.17511410.1612116X-RAY DIFFRACTION100
2.3533-2.59010.19761450.18412092X-RAY DIFFRACTION100
2.5901-2.96480.20041430.18242120X-RAY DIFFRACTION100
2.9648-3.73470.20681510.16832143X-RAY DIFFRACTION100
3.7347-37.30180.1731570.15932251X-RAY DIFFRACTION100

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