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- PDB-5m18: Crystal structure of PBP2a from MRSA in the presence of Cefepime ... -

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Basic information

Entry
Database: PDB / ID: 5m18
TitleCrystal structure of PBP2a from MRSA in the presence of Cefepime ligand
ComponentsPenicillin-binding protein 2
KeywordsPenicillin binding protein / Staphylococcus aureus
Function / homology
Function and homology information


glycosyltransferase activity / penicillin binding / carboxypeptidase activity / response to antibiotic / membrane
Similarity search - Function
NTF2-like; domain 1 / Penicillin-binding protein 2a; domain 3 / NTF2-like N-terminal transpeptidase / NTF2-like N-terminal transpeptidase domain / Penicillin-binding protein 2a (Domain 2) / Penicillin-binding protein 2a (Domain 2) / Ribosomal Protein L30; Chain: A, / Penicillin-binding protein, dimerisation domain / Penicillin-binding Protein dimerisation domain / Penicillin-binding protein, dimerisation domain superfamily ...NTF2-like; domain 1 / Penicillin-binding protein 2a; domain 3 / NTF2-like N-terminal transpeptidase / NTF2-like N-terminal transpeptidase domain / Penicillin-binding protein 2a (Domain 2) / Penicillin-binding protein 2a (Domain 2) / Ribosomal Protein L30; Chain: A, / 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 / NTF2-like domain superfamily / Nuclear Transport Factor 2; Chain: A, / Beta-lactamase / DD-peptidase/beta-lactamase superfamily / Beta-lactamase/transpeptidase-like / Roll / Alpha-Beta Complex / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
: / beta-muramic acid / PBP2a family beta-lactam-resistant peptidoglycan transpeptidase MecA / MecA
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.98 Å
AuthorsMolina, R. / Batuecas, M.T. / Hermoso, J.A.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health1R01AI116548 United States
CitationJournal: J. Am. Chem. Soc. / Year: 2017
Title: Conformational Dynamics in Penicillin-Binding Protein 2a of Methicillin-Resistant Staphylococcus aureus, Allosteric Communication Network and Enablement of Catalysis.
Authors: Mahasenan, K.V. / Molina, R. / Bouley, R. / Batuecas, M.T. / Fisher, J.F. / Hermoso, J.A. / Chang, M. / Mobashery, S.
History
DepositionOct 7, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 8, 2017Provider: repository / Type: Initial release
Revision 1.1Feb 15, 2017Group: Database references
Revision 1.2Jan 31, 2018Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_struct_conn_angle / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _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_asym_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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Jan 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

Downloads & links

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Assembly

Deposited unit
A: Penicillin-binding protein 2
B: Penicillin-binding protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)147,6389
Polymers146,5732
Non-polymers1,0657
Water7,404411
1
A: Penicillin-binding protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,9886
Polymers73,2871
Non-polymers7015
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Penicillin-binding protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,6503
Polymers73,2871
Non-polymers3642
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)80.623, 101.195, 186.618
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 Penicillin-binding protein 2 / Penicillin-binding protein 2 prime


Mass: 73286.656 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Gene: mecA / Production host: Escherichia coli (E. coli) / References: UniProt: E2D9B8, UniProt: Q7DHH4*PLUS
#2: Chemical
ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Cd
#3: Sugar ChemComp-MUR / beta-muramic acid / muramic acid / Muramic acid


Type: D-saccharide, beta linking / Mass: 251.234 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H17NO7
IdentifierTypeProgram
b-D-GlcpN3IUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
MurSNFG CARBOHYDRATE SYMBOLGMML 1.0
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 411 / 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: 2.6 Å3/Da / Density % sol: 52.64 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 20% (vol/vol) PEG 550 monomethyl ether, 880 mM NaCl, 100mMHepes (pH 7.0 buffer), and 16mMCdCl2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Feb 12, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.98→186.62 Å / Num. obs: 100216 / % possible obs: 93.8 % / Observed criterion σ(I): 2 / Redundancy: 7.2 % / CC1/2: 0.99 / Rsym value: 0.04 / Net I/σ(I): 14.8
Reflection shellResolution: 1.98→2.09 Å / Redundancy: 7.1 % / Rmerge(I) obs: 0.38 / Mean I/σ(I) obs: 2.2 / CC1/2: 0.89 / % possible all: 91.9

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Processing

Software
NameVersionClassification
PHENIX(dev_2420: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1VQQ

1vqq


Resolution: 1.98→93.309 Å / SU ML: 0.3 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 32.05
RfactorNum. reflection% reflection
Rfree0.2528 1996 1.99 %
Rwork0.2053 --
obs0.2063 100216 93.66 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.98→93.309 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10234 0 39 411 10684
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00810506
X-RAY DIFFRACTIONf_angle_d1.02214146
X-RAY DIFFRACTIONf_dihedral_angle_d16.4976456
X-RAY DIFFRACTIONf_chiral_restr0.0621536
X-RAY DIFFRACTIONf_plane_restr0.0061825
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9793-2.02880.42281500.34517363X-RAY DIFFRACTION99
2.0288-2.08370.3366880.32294386X-RAY DIFFRACTION59
2.0837-2.1450.34651520.29197383X-RAY DIFFRACTION100
2.145-2.21420.32911490.26937378X-RAY DIFFRACTION100
2.2142-2.29340.32371070.26635257X-RAY DIFFRACTION71
2.2934-2.38520.30271510.25077394X-RAY DIFFRACTION100
2.3852-2.49380.31511520.24047444X-RAY DIFFRACTION100
2.4938-2.62530.34181500.237403X-RAY DIFFRACTION100
2.6253-2.78980.27151520.2287471X-RAY DIFFRACTION100
2.7898-3.00520.28941510.23077470X-RAY DIFFRACTION100
3.0052-3.30760.29751510.22427480X-RAY DIFFRACTION100
3.3076-3.78620.23021370.18566683X-RAY DIFFRACTION88
3.7862-4.77030.18981480.15067276X-RAY DIFFRACTION96
4.7703-93.41280.18241580.16677832X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: 5.4205 Å / Origin y: -13.2682 Å / Origin z: -45.2268 Å
111213212223313233
T0.2628 Å2-0.0254 Å2-0.0238 Å2-0.3457 Å20.0215 Å2--0.2976 Å2
L0.5544 °2-0.0839 °2-0.1594 °2-0.3253 °20.0942 °2--1.3314 °2
S0.0085 Å °0.0533 Å °-0.0446 Å °-0.0136 Å °0.0185 Å °0.0339 Å °0.0895 Å °-0.0307 Å °-0.024 Å °
Refinement TLS groupSelection details: all

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