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

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Basic information

Entry
Database: PDB / ID: 3vsl
TitleCrystal structure of penicillin-binding protein 3 (PBP3) from methicilin-resistant Staphylococcus aureus in the cefotaxime bound 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
CEFOTAXIME, C3' cleaved, open, bound form / Penicillin-binding protein 3 / Penicillin-binding protein 3
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 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 15, 2017Group: Non-polymer description

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)145,0644
Polymers144,2692
Non-polymers7952
Water4,612256
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5790 Å2
ΔGint-6 kcal/mol
Surface area54380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)143.031, 143.031, 189.610
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
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: Chemical ChemComp-CEF / CEFOTAXIME, C3' cleaved, open, bound form / Cefotaxime


Mass: 397.429 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H15N5O5S2 / Comment: antibiotic*YM
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 256 / 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: 3.36 Å3/Da / Density % sol: 63.4 %
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: Photon Factory / Beamline: BL-1A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Nov 2, 2011 / Details: Si 111
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.399→50 Å / Num. obs: 76011 / % possible obs: 98.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.7 % / Rmerge(I) obs: 0.111 / Net I/σ(I): 9.9
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allDiffraction-ID% possible all
2.4-2.442.30.463367189
2.44-2.492.80.4793510192.5
2.49-2.533.50.4843725197.3
2.53-2.593.90.4863738198
2.59-2.644.10.4773762198.3
2.64-2.74.20.4583759198.5
2.7-2.774.40.4533771198.6
2.77-2.854.60.4393766198.8
2.85-2.934.80.4123806198.8
2.93-3.025.20.3783793199.2
3.02-3.135.70.323804199.3
3.13-3.2660.2813849199.4
3.26-3.416.30.2223825199.1
3.41-3.586.90.1643844199.6
3.58-3.817.30.1223844199.4
3.81-4.17.60.0953889199.7
4.1-4.5280.0723891199.6
4.52-5.178.30.0613921199.6
5.17-6.518.20.0613967199.5
6.51-508.20.0344180199.3

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Processing

Software
NameVersionClassification
HKL-2000data collection
MOLREPphasing
PHENIX(phenix.refine: 1.7.2_869)refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→48.861 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.7185 / SU ML: 0.87 / σ(F): 1.44 / Phase error: 34.22 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.3156 3797 5 %RANDOM
Rwork0.2467 72094 --
obs0.2501 75891 98.24 %-
Solvent computationShrinkage radii: 0.6 Å / VDW probe radii: 0.9 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 64.929 Å2 / ksol: 0.362 e/Å3
Displacement parametersBiso max: 182.47 Å2 / Biso mean: 69.3511 Å2 / Biso min: 16.09 Å2
Baniso -1Baniso -2Baniso -3
1--2.1137 Å2-0 Å20 Å2
2---2.1137 Å2-0 Å2
3---4.2275 Å2
Refinement stepCycle: LAST / Resolution: 2.4→48.861 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9890 0 52 256 10198
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0110110
X-RAY DIFFRACTIONf_angle_d1.42213618
X-RAY DIFFRACTIONf_chiral_restr0.1041513
X-RAY DIFFRACTIONf_plane_restr0.0071761
X-RAY DIFFRACTIONf_dihedral_angle_d21.6083890
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 27

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.4-2.43040.44121210.40312369249089
2.4304-2.46240.37551250.36892447257292
2.4624-2.49610.40431270.35292528265594
2.4961-2.53170.37141250.33552609273498
2.5317-2.56950.35491470.34312619276698
2.5695-2.60970.37871210.34492663278498
2.6097-2.65250.40391600.33652610277098
2.6525-2.69820.38171380.33632662280099
2.6982-2.74730.35821320.32832628276099
2.7473-2.80010.38641490.31012665281499
2.8001-2.85720.41941520.30382648280099
2.8572-2.91940.33941530.30152664281799
2.9194-2.98730.37571340.28852659279399
2.9873-3.0620.31721170.28052695281299
3.062-3.14470.34811600.26572666282699
3.1447-3.23730.33211450.24622683282899
3.2373-3.34170.28031720.22912651282399
3.3417-3.46110.27721360.21612696283299
3.4611-3.59970.30911330.227727322865100
3.5997-3.76340.32451430.21112718286199
3.7634-3.96180.25731420.195227112853100
3.9618-4.20990.24731550.188327192874100
4.2099-4.53470.24851450.173427252870100
4.5347-4.99060.2721410.176327522893100
4.9906-5.71180.32841330.230628012934100
5.7118-7.19260.32121460.252728152961100
7.1926-48.87130.28811450.22222959310499
Refinement TLS params.Method: refined / Origin x: 34.6713 Å / Origin y: -38.9449 Å / Origin z: 6.611 Å
111213212223313233
T0.5895 Å20.1516 Å2-0.0952 Å2-0.3966 Å2-0.0142 Å2--0.1334 Å2
L0.5307 °2-0.0308 °2-0.245 °2-3.6657 °2-0.314 °2--0.3603 °2
S-0.201 Å °-0.1934 Å °0.0236 Å °0.9208 Å °0.3517 Å °-0.1619 Å °-0.0316 Å °0.0393 Å °-0.0575 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1ALLA46 - 678
2X-RAY DIFFRACTION1ALLB46 - 678
3X-RAY DIFFRACTION1ALLC2 - 1
4X-RAY DIFFRACTION1ALLS2 - 259

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