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- PDB-4bl3: Crystal structure of PBP2a clinical mutant N146K from MRSA -

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Basic information

Entry
Database: PDB / ID: 4bl3
TitleCrystal structure of PBP2a clinical mutant N146K from MRSA
ComponentsPENICILLIN BINDING PROTEIN 2 PRIME
KeywordsHYDROLASE / 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
: / beta-muramic acid / Penicillin binding protein 2 prime / Penicillin binding protein 2 prime
Similarity search - Component
Biological speciesSTAPHYLOCOCCUS AUREUS (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsOtero, L.H. / Rojas-Altuve, A. / Carrasco-Lopez, C. / Hermoso, J.A.
CitationJournal: J.Am.Chem.Soc. / Year: 2014
Title: Disruption of Allosteric Response as an Unprecedented Mechanism of Resistance to Antibiotics.
Authors: Fishovitz, J. / Rojas-Altuve, A. / Otero, L.H. / Dawley, M. / Carrasco-Lopez, C. / Chang, M. / Hermoso, J.A. / Mobashery, S.
History
DepositionApr 30, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 21, 2014Provider: repository / Type: Initial release
Revision 1.1Sep 10, 2014Group: Database references
Revision 1.2Jul 5, 2017Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type
Revision 1.3Jul 29, 2020Group: Data collection / Derived calculations ...Data collection / Derived calculations / Other / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_database_status / 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_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.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.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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Dec 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)147,71815
Polymers146,2872
Non-polymers1,43113
Water1,964109
1
A: PENICILLIN BINDING PROTEIN 2 PRIME
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,9158
Polymers73,1441
Non-polymers7727
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)73,8037
Polymers73,1441
Non-polymers6596
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)81.790, 102.390, 187.130
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 PRIME / PENICILLIN-BINDING PROTEIN 2A


Mass: 73143.641 Da / Num. of mol.: 2 / Fragment: RESIDUES 26-668 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) STAPHYLOCOCCUS AUREUS (bacteria) / Strain: MU50 / 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
#2: Chemical
ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 7 / 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: 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
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 109 / 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: 2.68 Å3/Da / Density % sol: 54.07 % / Description: NONE
Crystal growpH: 7 / Details: pH 7

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.54179
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54179 Å / Relative weight: 1
ReflectionResolution: 3→69.07 Å / Num. obs: 30067 / % possible obs: 83.2 % / Observed criterion σ(I): 2 / Redundancy: 3.6 % / Biso Wilson estimate: 70.72 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 8.3
Reflection shellResolution: 3→3.16 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.58 / Mean I/σ(I) obs: 1.9 / % possible all: 75.3

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Processing

Software
NameVersionClassification
BUSTER2.10.0refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1VQQ
Resolution: 3→48.74 Å / Cor.coef. Fo:Fc: 0.9066 / Cor.coef. Fo:Fc free: 0.8571 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.6
Details: DISORDERED REGIONS WERE NOT MODELED. IDEAL-DIST CONTACT TERM CONTACT SETUP. RESIDUE TYPES WITHOUT CCP4 ATOM TYPE IN LIBRARY=CD CL. NUMBER OF ATOMS WITH PROPER CCP4 ATOM TYPE=10421. NUMBER ...Details: DISORDERED REGIONS WERE NOT MODELED. IDEAL-DIST CONTACT TERM CONTACT SETUP. RESIDUE TYPES WITHOUT CCP4 ATOM TYPE IN LIBRARY=CD CL. NUMBER OF ATOMS WITH PROPER CCP4 ATOM TYPE=10421. NUMBER WITH APPROX DEFAULT CCP4 ATOM TYPE=4. NUMBER TREATED BY BAD NON-BONDED CONTACTS=7.
RfactorNum. reflection% reflectionSelection details
Rfree0.3039 1866 7.07 %RANDOM
Rwork0.2353 ---
obs0.2402 26396 81.93 %-
Displacement parametersBiso mean: 75.68 Å2
Baniso -1Baniso -2Baniso -3
1--7.0295 Å20 Å20 Å2
2---3.1753 Å20 Å2
3---10.2048 Å2
Refine analyzeLuzzati coordinate error obs: 0.543 Å
Refinement stepCycle: LAST / Resolution: 3→48.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10273 0 45 109 10427
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0110477HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.214084HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d5065SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes349HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1429HARMONIC5
X-RAY DIFFRACTIONt_it10477HARMONIC20
X-RAY DIFFRACTIONt_nbd5SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion2.67
X-RAY DIFFRACTIONt_other_torsion3.86
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion1363SEMIHARMONIC5
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_contact11948SEMIHARMONIC4
LS refinement shellResolution: 3→3.12 Å / Total num. of bins used: 13
RfactorNum. reflection% reflection
Rfree0.3955 188 7.17 %
Rwork0.2961 2434 -
all0.3032 2622 -
obs--81.93 %
Refinement TLS params.

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

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
10.4709-0.06840.08520.33380.30472.4569-0.12110.0028-0.0440.09460.05650.01950.48410.28470.0646-0.09310.11080.01280.43530.0311-0.207318.302428.988851.7964
20.9798-0.0299-1.01730.20340.28032.2580.00590.09890.07810.0287-0.03260.0322-0.1035-0.28140.0267-0.16370.0622-0.02360.49520.0561-0.1987-8.170246.525644.269
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A
2X-RAY DIFFRACTION2CHAIN B

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