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

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Basic information

Entry
Database: PDB / ID: 5zqe
TitleCrystal Structure of Penicillin-Binding Protein D2 from Listeria monocytogenes in the Cefuroxime bound form
ComponentsLmo2812 protein
KeywordsANTIBIOTIC / penicillin-binding protein D2 / Listeria monocytogenes / antibiotics / beta-lactams / DD-carboxypeptidase / lmo2812 / LmPBPD2
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
Chem-CES / DI(HYDROXYETHYL)ETHER / Lmo2812 protein
Similarity search - Component
Biological speciesListeria monocytogenes EGD-e (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.996 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 / 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 1.4Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Lmo2812 protein
B: Lmo2812 protein
C: Lmo2812 protein
D: Lmo2812 protein
E: Lmo2812 protein
F: Lmo2812 protein
G: Lmo2812 protein
H: Lmo2812 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)245,37933
Polymers240,7338
Non-polymers4,64725
Water16,592921
1
A: Lmo2812 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,6594
Polymers30,0921
Non-polymers5683
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area640 Å2
ΔGint0 kcal/mol
Surface area10960 Å2
MethodPISA
2
B: Lmo2812 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,6594
Polymers30,0921
Non-polymers5683
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area670 Å2
ΔGint-1 kcal/mol
Surface area10900 Å2
MethodPISA
3
C: Lmo2812 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,6594
Polymers30,0921
Non-polymers5683
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area860 Å2
ΔGint-0 kcal/mol
Surface area10550 Å2
MethodPISA
4
D: Lmo2812 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,6594
Polymers30,0921
Non-polymers5683
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area640 Å2
ΔGint-0 kcal/mol
Surface area10640 Å2
MethodPISA
5
E: Lmo2812 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,5673
Polymers30,0921
Non-polymers4752
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area630 Å2
ΔGint0 kcal/mol
Surface area10710 Å2
MethodPISA
6
F: Lmo2812 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,7515
Polymers30,0921
Non-polymers6604
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area630 Å2
ΔGint0 kcal/mol
Surface area10700 Å2
MethodPISA
7
G: Lmo2812 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,8576
Polymers30,0921
Non-polymers7665
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area960 Å2
ΔGint-0 kcal/mol
Surface area10610 Å2
MethodPISA
8
H: Lmo2812 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,5673
Polymers30,0921
Non-polymers4752
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area700 Å2
ΔGint0 kcal/mol
Surface area10570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.041, 99.258, 155.050
Angle α, β, γ (deg.)90.00, 103.93, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Lmo2812 protein


Mass: 30091.605 Da / Num. of mol.: 8 / Fragment: UNP residues 21-272
Source method: isolated from a genetically manipulated source
Details: it contains covalently bound cefuroxime molecules
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-CES / 2-[CARBOXY-(2-FURAN-2-YL-2-METHOXYIMINO-ACETYLAMINO)-METHYL]-5-METHYL-3,6-DIHYDRO-2H-[1,3]THIAZINE-4-CARBOXYLIC ACID / CEFUROXIME (INHIBITION FORM)


Mass: 383.376 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C15H17N3O7S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


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


Mass: 18.015 Da / Num. of mol.: 921 / 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: 2.33 Å3/Da / Density % sol: 47.17 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7

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Data collection

DiffractionMean temperature: 200 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.9794 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 23, 2016
RadiationMonochromator: Double crystal SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 1.996→29.982 Å / Num. obs: 149025 / % possible obs: 91.13 % / Observed criterion σ(I): 0 / Redundancy: 6.1 % / Biso Wilson estimate: 13.29 Å2 / Rsym value: 0.127 / Net I/σ(I): 11.7
Reflection shellResolution: 1.996→2.067 Å / Redundancy: 5.9 % / Num. unique obs: 14478 / Rsym value: 0.475 / % possible all: 84.24

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5ZQA

5zqa


Resolution: 1.996→29.982 Å / Cross valid method: NONE / σ(F): 0 / Phase error: 38.41
RfactorNum. reflection% reflection
Rfree0.2362 2011 1.35 %
Rwork0.1991 --
obs0.2037 149025 99.42 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.996→29.982 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14942 0 303 921 16166
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00615436
X-RAY DIFFRACTIONf_angle_d0.82120819
X-RAY DIFFRACTIONf_dihedral_angle_d4.6219351
X-RAY DIFFRACTIONf_chiral_restr0.0452446
X-RAY DIFFRACTIONf_plane_restr0.0052650
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9962-2.04610.30671390.264610098X-RAY DIFFRACTION94
2.0461-2.10140.31741430.258310453X-RAY DIFFRACTION98
2.1014-2.16320.29961440.245910468X-RAY DIFFRACTION98
2.1632-2.2330.27191390.234310438X-RAY DIFFRACTION98
2.233-2.31280.29921450.228410538X-RAY DIFFRACTION98
2.3128-2.40540.27181420.231110442X-RAY DIFFRACTION98
2.4054-2.51480.27981410.223510520X-RAY DIFFRACTION98
2.5148-2.64730.31061460.220610542X-RAY DIFFRACTION98
2.6473-2.8130.25721450.209610498X-RAY DIFFRACTION98
2.813-3.030.20531440.197210569X-RAY DIFFRACTION98
3.03-3.33450.22141450.183510483X-RAY DIFFRACTION98
3.3345-3.81610.21291430.174810600X-RAY DIFFRACTION99
3.8161-4.80430.17061450.158610604X-RAY DIFFRACTION99
4.8043-28.99050.20481470.186110747X-RAY DIFFRACTION99

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