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- PDB-3vsk: Crystal structure of penicillin-binding protein 3 (PBP3) from met... -

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Basic information

Entry
Database: PDB / ID: 3vsk
TitleCrystal structure of penicillin-binding protein 3 (PBP3) from methicilin-resistant Staphylococcus aureus in the apo form.
ComponentsPenicillin-binding protein 3
KeywordsPENICILLIN-BINDING PROTEIN / penicillin-binding domain / Transpeptidase
Function / homology
Function and homology information


penicillin binding / membrane => GO:0016020 / membrane
Similarity search - Function
Penicillin-binding protein, N-terminal non-catalytic domain, head sub-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 / Penicillin-binding protein, transpeptidase / Penicillin binding protein transpeptidase domain / Beta-lactamase / DD-peptidase/beta-lactamase superfamily ...Penicillin-binding protein, N-terminal non-catalytic domain, head sub-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 / Penicillin-binding protein, transpeptidase / Penicillin binding protein transpeptidase domain / Beta-lactamase / DD-peptidase/beta-lactamase superfamily / Beta-lactamase/transpeptidase-like / Arc Repressor Mutant, subunit A / Alpha-Beta Complex / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Penicillin-binding protein 3 / Penicillin-binding protein 3
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 2.301 Å
AuthorsYoshida, H. / Tame, J.R. / Park, S.Y.
CitationJournal: J.Mol.Biol. / Year: 2012
Title: Crystal Structures of Penicillin-Binding Protein 3 (PBP3) from Methicillin-Resistant Staphylococcus aureus in the Apo and Cefotaxime-Bound Forms.
Authors: Yoshida, H. / Kawai, F. / Obayashi, E. / Akashi, S. / Roper, D.I. / Tame, J.R. / Park, S.Y.
History
DepositionApr 25, 2012Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 31, 2012Provider: repository / Type: Initial release
Revision 1.1Mar 20, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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 3
B: Penicillin-binding protein 3


Theoretical massNumber of molelcules
Total (without water)144,2692
Polymers144,2692
Non-polymers00
Water4,684260
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4360 Å2
ΔGint-5 kcal/mol
Surface area54780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)143.419, 143.419, 189.359
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein Penicillin-binding protein 3


Mass: 72134.734 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 46-691
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Strain: MW2 / Gene: pbp3, MW1504 / Plasmid: pET28b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q8NWC2, UniProt: A0A0H3K0B9*PLUS
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 260 / 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: 3.37 Å3/Da / Density % sol: 63.55 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 2.0M Ammonium sulfate, 0.5M Lithium chloride, 5% Glycerol, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
DetectorType: MX225HE / Detector: CCD / Date: Feb 15, 2011 / Details: Si 111
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. obs: 85132 / % possible obs: 96.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.7 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 11.2
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allDiffraction-ID% possible all
2.3-2.3830.4947754189.4
2.38-2.483.40.478120193.5
2.48-2.593.70.4418201194.7
2.59-2.734.20.3918425196.8
2.73-2.94.80.338533197.7
2.9-3.125.70.238657198.9
3.12-3.446.70.1458711199.3
3.44-3.937.80.0888741199.3
3.93-4.9580.088853199.1
4.95-508.80.0499137198.4

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Processing

Software
NameVersionClassification
HKL-2000data collection
SHARPphasing
PHENIX(phenix.refine: 1.7.2_869)refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MIR / Resolution: 2.301→40.903 Å / SU ML: 0.79 / σ(F): 0 / σ(I): 0 / Phase error: 32.9 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.3002 4274 5.02 %RANDOM
Rwork0.2609 ---
all0.2629 ---
obs0.2629 85097 96.81 %-
Solvent computationShrinkage radii: 0.6 Å / VDW probe radii: 0.9 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 65.648 Å2 / ksol: 0.345 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-0.2861 Å20 Å2-0 Å2
2--0.2861 Å20 Å2
3----0.9764 Å2
Refinement stepCycle: LAST / Resolution: 2.301→40.903 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9890 0 0 260 10150
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0110053
X-RAY DIFFRACTIONf_angle_d1.46113541
X-RAY DIFFRACTIONf_dihedral_angle_d21.2953883
X-RAY DIFFRACTIONf_chiral_restr0.1071499
X-RAY DIFFRACTIONf_plane_restr0.0071756
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.3006-2.32670.40551210.4051243288
2.3267-2.35410.40541070.3946248389
2.3541-2.38280.36221340.3785246191
2.3828-2.4130.39911350.3658255293
2.413-2.44470.39291160.3473257093
2.4447-2.47820.35641520.3347260695
2.4782-2.51360.35081610.3359255194
2.5136-2.55110.36041300.3299260795
2.5511-2.5910.38651530.3145259295
2.591-2.63340.34651170.3113268996
2.6334-2.67880.34471400.3098264196
2.6788-2.72750.37021310.3028270698
2.7275-2.780.35911430.307270698
2.78-2.83670.32891370.3045269598
2.8367-2.89840.35991520.3104270098
2.8984-2.96580.37951310.2885274599
2.9658-3.03990.31431480.2777271999
3.0399-3.12210.34061590.2728275099
3.1221-3.21390.27721490.2691275099
3.2139-3.31760.31581620.2773271999
3.3176-3.43620.32351450.261278299
3.4362-3.57370.32191550.2487275399
3.5737-3.73620.26141510.2362276099
3.7362-3.9330.26441440.2192278299
3.933-4.17920.26951520.2135277899
4.1792-4.50150.26261460.1975280999
4.5015-4.95380.23281400.1939282199
4.9538-5.66910.30281660.2383280299
5.6691-7.13620.29851360.2619287599
7.1362-40.9090.23751610.243298798

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