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- PDB-6g9f: Structural basis for the inhibition of E. coli PBP2 -

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Basic information

Entry
Database: PDB / ID: 6g9f
TitleStructural basis for the inhibition of E. coli PBP2
ComponentsPeptidoglycan D,D-transpeptidase MrdA
KeywordsHYDROLASE/ANTIBIOTIC / penicillin binding protein / HYDROLASE-ANTIBIOTIC COMPLEX
Function / homology
Function and homology information


peptidoglycan L,D-transpeptidase activity / serine-type D-Ala-D-Ala carboxypeptidase / serine-type D-Ala-D-Ala carboxypeptidase activity / penicillin binding / peptidoglycan biosynthetic process / cell wall organization / outer membrane-bounded periplasmic space / regulation of cell shape / response to antibiotic / proteolysis / plasma membrane
Similarity search - Function
Penicillin-binding protein 2 / 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
Chem-NXL / Peptidoglycan D,D-transpeptidase MrdA
Similarity search - Component
Biological speciesEscherichia coli K-12 (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.35 Å
AuthorsRuff, M. / Levy, N.
CitationJournal: J.Med.Chem. / Year: 2019
Title: Structural Basis for E. coli Penicillin Binding Protein (PBP) 2 Inhibition, a Platform for Drug Design.
Authors: Levy, N. / Bruneau, J.M. / Le Rouzic, E. / Bonnard, D. / Le Strat, F. / Caravano, A. / Chevreuil, F. / Barbion, J. / Chasset, S. / Ledoussal, B. / Moreau, F. / Ruff, M.
History
DepositionApr 10, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 22, 2019Provider: repository / Type: Initial release
Revision 1.1Feb 5, 2020Group: Database references / Source and taxonomy
Category: entity_src_gen / struct_ref ...entity_src_gen / struct_ref / struct_ref_seq / struct_ref_seq_dif
Item: _entity_src_gen.pdbx_gene_src_gene / _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id ..._entity_src_gen.pdbx_gene_src_gene / _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id / _entity_src_gen.pdbx_gene_src_scientific_name / _struct_ref.db_code / _struct_ref.pdbx_db_accession / _struct_ref_seq.pdbx_db_accession / _struct_ref_seq_dif.pdbx_seq_db_accession_code
Revision 1.2Jan 17, 2024Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Peptidoglycan D,D-transpeptidase MrdA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,0762
Polymers62,8091
Non-polymers2671
Water2,216123
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area24270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)125.078, 182.875, 74.767
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-734-

HOH

21A-770-

HOH

31A-796-

HOH

41A-808-

HOH

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Components

#1: Protein Peptidoglycan D,D-transpeptidase MrdA / Penicillin-binding protein 2 / PBP-2


Mass: 62809.215 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: The Ser 330 in the structure is modified covalently and is named (S31)
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Gene: mrdA, pbpA, b0635, JW0630 / Production host: Escherichia coli BL21 (bacteria)
References: UniProt: P0AD65, serine-type D-Ala-D-Ala carboxypeptidase
#2: Chemical ChemComp-NXL / (2S,5R)-1-formyl-5-[(sulfooxy)amino]piperidine-2-carboxamide / avibactam, bound form / NXL104, bound form / Avibactam


Mass: 267.260 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H13N3O6S / Comment: antibiotic, inhibitor*YM
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 123 / 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: 3.38 Å3/Da / Density % sol: 63.56 %
Crystal growTemperature: 300 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.1 M TrisBase / Bicine pH 8,5 ; 0.1 M [Carboxylic acids mix (0.02 M Sodium formate ; 0.02 M Ammonium acetate ; 0.02 M Sodium citrate tribasic dihydrate ; 0.02 M Sodium potassium tartrate ...Details: 0.1 M TrisBase / Bicine pH 8,5 ; 0.1 M [Carboxylic acids mix (0.02 M Sodium formate ; 0.02 M Ammonium acetate ; 0.02 M Sodium citrate tribasic dihydrate ; 0.02 M Sodium potassium tartrate tetrahydrate ; 0.02 M Sodium oxamate) ; 24 % Glycerol ; 12 % PEG 4000] equilibrated against 2.0 M NaCl

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-X / Wavelength: 1.5418 Å
DetectorType: DECTRIS EIGER R 4M / Detector: PIXEL / Date: Feb 8, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.35→39.005 Å / Num. obs: 35810 / % possible obs: 98.67 % / Redundancy: 5.5 % / CC1/2: 0.996 / Rmerge(I) obs: 0.1454 / Rpim(I) all: 0.06713 / Rrim(I) all: 0.1607 / Net I/σ(I): 7.87
Reflection shellResolution: 2.35→2.434 Å / Redundancy: 5.6 % / Rmerge(I) obs: 2.546 / Num. unique obs: 3525 / CC1/2: 0.419 / Rpim(I) all: 1.167 / Rrim(I) all: 2.809 / % possible all: 95.57

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6G9S
Resolution: 2.35→39.01 Å / SU ML: 0.36 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 28.04
RfactorNum. reflection% reflection
Rfree0.248 3754 5.6 %
Rwork0.199 --
obs0.201 35639 97.1 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.35→39.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4262 0 17 123 4402
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0084386
X-RAY DIFFRACTIONf_angle_d0.9715965
X-RAY DIFFRACTIONf_dihedral_angle_d6.2852622
X-RAY DIFFRACTIONf_chiral_restr0.053646
X-RAY DIFFRACTIONf_plane_restr0.007774
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3498-2.37950.36111040.31941817X-RAY DIFFRACTION77
2.3795-2.41080.31921290.32232203X-RAY DIFFRACTION89
2.4108-2.44380.3671350.32432208X-RAY DIFFRACTION94
2.4438-2.47870.42031440.31732394X-RAY DIFFRACTION98
2.4787-2.51570.31421390.30722419X-RAY DIFFRACTION99
2.5157-2.5550.33951400.31342368X-RAY DIFFRACTION99
2.555-2.59690.35361420.30442395X-RAY DIFFRACTION99
2.5969-2.64170.33351400.30252413X-RAY DIFFRACTION100
2.6417-2.68970.37851460.29982415X-RAY DIFFRACTION100
2.6897-2.74140.28051420.27812384X-RAY DIFFRACTION99
2.7414-2.79740.28451420.27332347X-RAY DIFFRACTION99
2.7974-2.85820.30321450.25842449X-RAY DIFFRACTION100
2.8582-2.92460.30751430.24682391X-RAY DIFFRACTION99
2.9246-2.99770.28811460.24032427X-RAY DIFFRACTION100
2.9977-3.07880.32241390.23942363X-RAY DIFFRACTION99
3.0788-3.16930.29381440.24852424X-RAY DIFFRACTION99
3.1693-3.27160.30641370.222354X-RAY DIFFRACTION99
3.2716-3.38840.29641390.21132405X-RAY DIFFRACTION99
3.3884-3.5240.23931390.20122358X-RAY DIFFRACTION98
3.524-3.68430.24681400.18132360X-RAY DIFFRACTION98
3.6843-3.87840.24521370.17692361X-RAY DIFFRACTION97
3.8784-4.12110.25641340.16442324X-RAY DIFFRACTION97
4.1211-4.43890.19691390.15192390X-RAY DIFFRACTION97
4.4389-4.88480.16161390.14032292X-RAY DIFFRACTION97
4.8848-5.58990.19751450.15082333X-RAY DIFFRACTION96
5.5899-7.0360.22711430.17422331X-RAY DIFFRACTION97
7.036-39.00990.17811420.15332343X-RAY DIFFRACTION97
Refinement TLS params.Method: refined / Origin x: 28.995 Å / Origin y: 55.231 Å / Origin z: 38.5428 Å
111213212223313233
T0.371 Å2-0.0529 Å2-0.0141 Å2-0.3825 Å20.0071 Å2--0.3007 Å2
L1.5106 °21.4841 °20.2467 °2-1.9455 °20.0109 °2--0.0129 °2
S0.035 Å °0.0046 Å °0.0023 Å °-0.0278 Å °-0.0026 Å °0.046 Å °0.0582 Å °-0.0198 Å °-0.0001 Å °
Refinement TLS groupSelection details: ALL

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