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- PDB-4bl2: Crystal structure of PBP2a clinical mutant E150K from MRSA -

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Basic information

Entry
Database: PDB / ID: 4bl2
TitleCrystal structure of PBP2a clinical mutant E150K from MRSA
ComponentsPENICILLIN BINDING PROTEIN 2 PRIME
KeywordsHYDROLASE / PENICILLIN BINDING PROTEINS / B-LACTUM ANTIBIOTICS
Function / homology
Function and homology information


penicillin binding / response to antibiotic / membrane => GO:0016020
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) / Penicillin-binding protein, dimerisation domain / Penicillin-binding Protein dimerisation domain / Penicillin-binding protein, dimerisation domain superfamily / Ribosomal Protein L30; Chain: A, ...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) / Penicillin-binding protein, dimerisation domain / Penicillin-binding Protein dimerisation domain / Penicillin-binding protein, dimerisation domain superfamily / Ribosomal Protein L30; Chain: A, / Penicillin binding protein transpeptidase domain / Penicillin-binding protein, transpeptidase / NTF2-like domain superfamily / Nuclear Transport Factor 2; Chain: A, / DD-peptidase/beta-lactamase superfamily / Beta-lactamase / Beta-lactamase/transpeptidase-like / Roll / Alpha-Beta Complex / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
: / Penicillin binding protein 2 prime / Penicillin binding protein 2 prime
Similarity search - Component
Biological speciesSTAPHYLOCOCCUS AUREUS (unknown)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.72 Å
AuthorsOtero, L.H. / Rojas-Altuve, A. / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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)147,76113
Polymers146,8322
Non-polymers92911
Water3,891216
1
A: PENICILLIN BINDING PROTEIN 2 PRIME
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,9367
Polymers73,4161
Non-polymers5216
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)73,8246
Polymers73,4161
Non-polymers4085
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)81.437, 101.637, 186.838
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: 73415.906 Da / Num. of mol.: 2 / Fragment: RESIDUES 26-668 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) STAPHYLOCOCCUS AUREUS (unknown) / 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: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 216 / 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: 2.63 Å3/Da / Density % sol: 53.29 % / 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: 2.72→19.89 Å / Num. obs: 42164 / % possible obs: 99.2 % / Observed criterion σ(I): 2 / Redundancy: 14.1 % / Biso Wilson estimate: 55.6 Å2 / Rmerge(I) obs: 0.13 / Net I/σ(I): 16.1
Reflection shellResolution: 2.72→2.87 Å / Redundancy: 11.4 % / Rmerge(I) obs: 0.4 / Mean I/σ(I) obs: 7.5 / % possible all: 96.6

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Processing

Software
NameVersionClassification
BUSTER2.10.0refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1VQQ
Resolution: 2.72→19.89 Å / Cor.coef. Fo:Fc: 0.9273 / Cor.coef. Fo:Fc free: 0.8577 / SU R Cruickshank DPI: 5.047 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.383 / SU Rfree Cruickshank DPI: 0.39 / Details: DISORDERED REGIONS WERE NOT MODELED
RfactorNum. reflection% reflectionSelection details
Rfree0.2867 3004 7.16 %RANDOM
Rwork0.2067 ---
obs0.2123 41942 99.1 %-
Displacement parametersBiso mean: 53 Å2
Baniso -1Baniso -2Baniso -3
1-4.555 Å20 Å20 Å2
2---8.8355 Å20 Å2
3---4.2805 Å2
Refine analyzeLuzzati coordinate error obs: 0.416 Å
Refinement stepCycle: LAST / Resolution: 2.72→19.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10226 0 11 216 10453
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0110396HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.1713979HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d5033SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes348HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1422HARMONIC5
X-RAY DIFFRACTIONt_it10396HARMONIC20
X-RAY DIFFRACTIONt_nbd2SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion2.87
X-RAY DIFFRACTIONt_other_torsion3.8
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion1359SEMIHARMONIC5
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_contact11412SEMIHARMONIC4
LS refinement shellResolution: 2.72→2.79 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.4074 229 7.96 %
Rwork0.3004 2648 -
all0.3089 2877 -
obs--99.1 %
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)
10.2586-0.07110.31930.08730.07732.8003-0.02570.0143-0.02710.02780.03940.02930.38990.1679-0.0136-0.06230.040.01620.30970.0193-0.200318.214528.668551.6581
20.87140.0502-1.02010.11240.11331.89720.0580.06070.0306-0.0205-0.04830.0322-0.1539-0.1548-0.0097-0.10090.0319-0.00330.3390.0325-0.2031-7.856346.098244.1112
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A
2X-RAY DIFFRACTION2CHAIN B

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