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- PDB-3zfz: Crystal structure of ceftaroline acyl-PBP2a from MRSA with non- c... -

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Basic information

Entry
Database: PDB / ID: 3zfz
TitleCrystal structure of ceftaroline acyl-PBP2a from MRSA with non- covalently bound ceftaroline and muramic acid at allosteric site obtained by soaking
ComponentsPENICILLIN BINDING PROTEIN 2 PRIME
KeywordsHYDROLASE / PENICILLIN BINDING PROTEINS / MRSA / ALLOSTERIC SITE / B-LACTAM ANTIBIOTICS
Function / homology
Function and homology information


penicillin binding / membrane => GO:0016020 / 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
Ceftaroline / Ceftaroline, bound form / : / beta-muramic acid / Penicillin binding protein 2 prime / Penicillin binding protein 2 prime
Similarity search - Component
Biological speciesSTAPHYLOCOCCUS AUREUS SUBSP. AUREUS MU50 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 Å
AuthorsOtero, L.H. / Rojas-Altuve, A. / Hermoso, J.A.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2013
Title: How Allosteric Control of Staphylococcus Aureus Penicillin Binding Protein 2A Enables Methicillin Resistance and Physiological Function
Authors: Otero, L.H. / Rojas-Altuve, A. / Llarrull, L.I. / Carrasco-Lopez, C. / Kumarasiri, M. / Lastochkin, E. / Fishovitz, J. / Dawley, M. / Hesek, D. / Lee, M. / Johnson, J.W. / Fisher, J.F. / ...Authors: Otero, L.H. / Rojas-Altuve, A. / Llarrull, L.I. / Carrasco-Lopez, C. / Kumarasiri, M. / Lastochkin, E. / Fishovitz, J. / Dawley, M. / Hesek, D. / Lee, M. / Johnson, J.W. / Fisher, J.F. / Chang, M. / Mobashery, S. / Hermoso, J.A.
History
DepositionDec 13, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 9, 2013Provider: repository / Type: Initial release
Revision 1.1Oct 30, 2013Group: Database references
Revision 1.2Jul 29, 2020Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Other / Structure summary
Category: chem_comp / citation ...chem_comp / citation / database_PDB_caveat / entity / pdbx_chem_comp_identifier / pdbx_database_status / pdbx_entity_nonpoly / pdbx_struct_conn_angle / struct_conn / struct_conn_type / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _citation.page_last / _entity.pdbx_description / _pdbx_database_status.status_code_sf / _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.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_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.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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.ptnr1_symmetry / _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 / _struct_conn_type.id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3Dec 20, 2023Group: 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 PRIME
B: PENICILLIN BINDING PROTEIN 2 PRIME
hetero molecules


Theoretical massNumber of molelcules
Total (without water)149,33018
Polymers146,5732
Non-polymers2,75716
Water11,998666
1
A: PENICILLIN BINDING PROTEIN 2 PRIME
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,38411
Polymers73,2871
Non-polymers2,09810
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: PENICILLIN BINDING PROTEIN 2 PRIME
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,9467
Polymers73,2871
Non-polymers6596
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)80.520, 101.480, 187.010
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein / Sugars , 2 types, 4 molecules AB

#1: Protein PENICILLIN BINDING PROTEIN 2 PRIME / PENICILLIN-BINDING PROTEIN 2A


Mass: 73286.656 Da / Num. of mol.: 2 / Fragment: RESIDUES 27-668
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) STAPHYLOCOCCUS AUREUS SUBSP. AUREUS MU50 (bacteria)
Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): STAR
References: UniProt: Q54113, UniProt: A0A0H3JPA5*PLUS, serine-type D-Ala-D-Ala carboxypeptidase
#6: 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

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Non-polymers , 5 types, 680 molecules

#2: Chemical
ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Cd
#3: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-AI8 / Ceftaroline, bound form


Mass: 607.729 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C22H23N8O5S4
#5: Chemical ChemComp-1W8 / Ceftaroline / Ceftaroline fosamil


Mass: 605.713 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C22H21N8O5S4 / Comment: antibiotic*YM
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 666 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.61 Å3/Da / Density % sol: 52.82 % / Description: NONE
Crystal growpH: 7 / Details: pH 7

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Type: SLS / Wavelength: 1
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.25→68.76 Å / Num. obs: 73548 / % possible obs: 100 % / Observed criterion σ(I): 2 / Redundancy: 6 % / Biso Wilson estimate: 40 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 16.7
Reflection shellResolution: 2.25→2.37 Å / Redundancy: 6.7 % / Rmerge(I) obs: 0.69 / Mean I/σ(I) obs: 3.1 / % possible all: 100

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Processing

Software
NameVersionClassification
BUSTER2.10.0refinement
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1VQQ

1vqq


Resolution: 2.25→68.76 Å / Cor.coef. Fo:Fc: 0.9343 / Cor.coef. Fo:Fc free: 0.9093 / SU R Cruickshank DPI: 0.267 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.278 / SU Rfree Blow DPI: 0.218 / SU Rfree Cruickshank DPI: 0.217
Details: IDEAL-DIST CONTACT TERM CONTACT SETUP. RESIDUE TYPES WITHOUT CCP4 ATOM TYPE IN LIBRARY=CD CL.NUMBER OF ATOMS WITH PROPER CCP4 ATOM TYPE=11058. NUMBER WITH APPROX DEFAULT CCP4 ATOM TYPE=4. ...Details: IDEAL-DIST CONTACT TERM CONTACT SETUP. RESIDUE TYPES WITHOUT CCP4 ATOM TYPE IN LIBRARY=CD CL.NUMBER OF ATOMS WITH PROPER CCP4 ATOM TYPE=11058. NUMBER WITH APPROX DEFAULT CCP4 ATOM TYPE=4.NUMBER TREATED BY BAD NON-BONDED CONTACTS=8.
RfactorNum. reflection% reflectionSelection details
Rfree0.249 5315 7.24 %RANDOM
Rwork0.1937 ---
obs0.1977 73460 99.99 %-
Displacement parametersBiso mean: 66.89 Å2
Baniso -1Baniso -2Baniso -3
1--0.8092 Å20 Å20 Å2
2---0.5122 Å20 Å2
3---1.3213 Å2
Refine analyzeLuzzati coordinate error obs: 0.346 Å
Refinement stepCycle: LAST / Resolution: 2.25→68.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10247 0 124 666 11037
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0110570HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.2114247HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d5059SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes352HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1437HARMONIC5
X-RAY DIFFRACTIONt_it10570HARMONIC20
X-RAY DIFFRACTIONt_nbd6SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion3.22
X-RAY DIFFRACTIONt_other_torsion3.49
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion1360SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact12468SEMIHARMONIC4
LS refinement shellResolution: 2.25→2.31 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.3002 367 6.85 %
Rwork0.2494 4993 -
all0.253 5360 -
obs--99.99 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.2879-0.01870.33560.2229-0.2542.49960.00730.0235-0.0525-0.0351-0.00280.00820.25150.13-0.0045-0.01760.0240.00140.5305-0.0130.010618.056228.874451.8598
21.0103-0.0126-1.12190.18650.17191.8650.09390.03280.0311-0.0371-0.0680.0379-0.2074-0.0926-0.0259-0.00090.0381-0.02470.56890.0315-0.0095-7.90546.269543.9995
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A
2X-RAY DIFFRACTION2CHAIN B

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