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- PDB-5m19: Crystal structure of PBP2a from MRSA in the presence of Oxacillin... -

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Basic information

Entry
Database: PDB / ID: 5m19
TitleCrystal structure of PBP2a from MRSA in the presence of Oxacillin ligand
ComponentsPenicillin-binding protein 2
KeywordsPenicillin binding protein / Staphylococcus aureus
Function / homology
Function and homology information


peptidoglycan L,D-transpeptidase activity / glycosyltransferase activity / penicillin binding / cell wall organization / response to antibiotic / plasma membrane
Similarity search - Function
Penicillin-binding protein 2a; domain 3 / NTF2-like; domain 1 / 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 2a; domain 3 / NTF2-like; domain 1 / 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 / Pbp2a
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 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 2.0Jan 31, 2018Group: Advisory / Atomic model ...Advisory / Atomic model / Author supporting evidence / Derived calculations
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / pdbx_audit_support / pdbx_struct_conn_angle / pdbx_validate_close_contact / struct_conn / struct_site
Item: _atom_site.auth_asym_id / _atom_site.auth_seq_id ..._atom_site.auth_asym_id / _atom_site.auth_seq_id / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_seq_id / _pdbx_audit_support.funding_organization / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_validate_close_contact.auth_seq_id_1 / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_site.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_seq_id
Revision 2.1Jul 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.ptnr2_symmetry / _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 / _struct_conn.ptnr2_symmetry
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.2Jun 16, 2021Group: Derived calculations / Refinement description / Structure summary
Category: chem_comp / pdbx_refine_tls_group ...chem_comp / pdbx_refine_tls_group / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop
Item: _chem_comp.pdbx_synonyms
Revision 2.3Jan 17, 2024Group: 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

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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)147,75010
Polymers146,5732
Non-polymers1,1778
Water11,746652
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)73,7634
Polymers73,2871
Non-polymers4763
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)80.499, 102.190, 185.682
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.: 6 / Source method: obtained synthetically / Formula: Cd
#3: Sugar ChemComp-MUR / beta-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


Mass: 18.015 Da / Num. of mol.: 652 / 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: 2.61 Å3/Da / Density % sol: 52.79 %
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 PILATUS 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: 2→49.07 Å / Num. obs: 197867 / % possible obs: 99.9 % / Observed criterion σ(I): 2 / Redundancy: 5.1 % / CC1/2: 0.99 / Rsym value: 0.03 / Net I/σ(I): 13.1
Reflection shellResolution: 2→2.03 Å / Redundancy: 4.1 % / CC1/2: 0.94 / % possible all: 99.8

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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: 2→46.42 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.9 / Phase error: 28.87
RfactorNum. reflection% reflection
Rfree0.2467 3819 1.93 %
Rwork0.1904 --
obs0.1914 197867 98.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2→46.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10216 0 40 652 10908
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00710466
X-RAY DIFFRACTIONf_angle_d0.91414091
X-RAY DIFFRACTIONf_dihedral_angle_d16.5116429
X-RAY DIFFRACTIONf_chiral_restr0.0591532
X-RAY DIFFRACTIONf_plane_restr0.0051817
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.02530.33891380.26717207X-RAY DIFFRACTION100
2.0253-2.0520.3161440.25657169X-RAY DIFFRACTION99
2.052-2.08010.31291420.26247219X-RAY DIFFRACTION99
2.0801-2.10980.30931430.24517194X-RAY DIFFRACTION99
2.1098-2.14130.28151390.23487240X-RAY DIFFRACTION99
2.1413-2.17480.28451410.23917236X-RAY DIFFRACTION99
2.1748-2.21040.34511410.21847163X-RAY DIFFRACTION99
2.2104-2.24850.2661420.26267067X-RAY DIFFRACTION97
2.2485-2.28940.34371400.22837056X-RAY DIFFRACTION98
2.2894-2.33340.27581390.21387192X-RAY DIFFRACTION99
2.3334-2.38110.24941440.20617193X-RAY DIFFRACTION98
2.3811-2.43280.27891460.20417161X-RAY DIFFRACTION99
2.4328-2.48940.28881400.2057251X-RAY DIFFRACTION100
2.4894-2.55170.28921380.20497249X-RAY DIFFRACTION100
2.5517-2.62070.28241450.20037223X-RAY DIFFRACTION100
2.6207-2.69780.311450.20247220X-RAY DIFFRACTION100
2.6978-2.78480.30011410.21137174X-RAY DIFFRACTION99
2.7848-2.88440.30641470.2147254X-RAY DIFFRACTION100
2.8844-2.99980.27711430.20617175X-RAY DIFFRACTION99
2.9998-3.13630.26321420.20197104X-RAY DIFFRACTION98
3.1363-3.30160.25231410.19857223X-RAY DIFFRACTION99
3.3016-3.50840.2061430.18527242X-RAY DIFFRACTION99
3.5084-3.77920.20981430.16297165X-RAY DIFFRACTION99
3.7792-4.15930.23221340.15777087X-RAY DIFFRACTION98
4.1593-4.76060.17681380.14067190X-RAY DIFFRACTION99
4.7606-5.99590.21561420.17037228X-RAY DIFFRACTION99
5.9959-46.4330.20141380.17667166X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: -5.4539 Å / Origin y: -13.3062 Å / Origin z: 45.2802 Å
111213212223313233
T0.2293 Å20.0264 Å2-0.0179 Å2-0.2157 Å2-0.0195 Å2--0.2498 Å2
L0.3549 °20.0419 °2-0.1398 °2-0.2779 °2-0.1083 °2--1.1829 °2
S-0.0037 Å °0.0099 Å °-0.0504 Å °-0.0099 Å °0.0172 Å °-0.0362 Å °0.1114 Å °0.0661 Å °-0.0156 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND ( RESID 27:668 OR RESID 701:705 OR RESID 801:1148 ) ) OR ( CHAIN B AND ( RESID 701:702 OR RESID 27:668 OR RESID 801:1104 OR RESID 703:703 ) )A27 - 668
2X-RAY DIFFRACTION1( CHAIN A AND ( RESID 27:668 OR RESID 701:705 OR RESID 801:1148 ) ) OR ( CHAIN B AND ( RESID 701:702 OR RESID 27:668 OR RESID 801:1104 OR RESID 703:703 ) )A701 - 705
3X-RAY DIFFRACTION1( CHAIN A AND ( RESID 27:668 OR RESID 701:705 OR RESID 801:1148 ) ) OR ( CHAIN B AND ( RESID 701:702 OR RESID 27:668 OR RESID 801:1104 OR RESID 703:703 ) )A801 - 1148
4X-RAY DIFFRACTION1( CHAIN A AND ( RESID 27:668 OR RESID 701:705 OR RESID 801:1148 ) ) OR ( CHAIN B AND ( RESID 701:702 OR RESID 27:668 OR RESID 801:1104 OR RESID 703:703 ) )B701 - 702
5X-RAY DIFFRACTION1( CHAIN A AND ( RESID 27:668 OR RESID 701:705 OR RESID 801:1148 ) ) OR ( CHAIN B AND ( RESID 701:702 OR RESID 27:668 OR RESID 801:1104 OR RESID 703:703 ) )B27 - 668
6X-RAY DIFFRACTION1( CHAIN A AND ( RESID 27:668 OR RESID 701:705 OR RESID 801:1148 ) ) OR ( CHAIN B AND ( RESID 701:702 OR RESID 27:668 OR RESID 801:1104 OR RESID 703:703 ) )B801 - 1104
7X-RAY DIFFRACTION1( CHAIN A AND ( RESID 27:668 OR RESID 701:705 OR RESID 801:1148 ) ) OR ( CHAIN B AND ( RESID 701:702 OR RESID 27:668 OR RESID 801:1104 OR RESID 703:703 ) )B703

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