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- PDB-3pbt: Crystal structure of PBP3 complexed with MC-1 -

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Basic information

Database: PDB / ID: 3pbt
TitleCrystal structure of PBP3 complexed with MC-1
ComponentsPenicillin-binding protein 3
Function / homology
Function and homology information

peptidoglycan glycosyltransferase activity / serine-type D-Ala-D-Ala carboxypeptidase / FtsZ-dependent cytokinesis / division septum assembly / serine-type D-Ala-D-Ala carboxypeptidase activity / penicillin binding / peptidoglycan biosynthetic process / cell wall organization / regulation of cell shape / plasma membrane => GO:0005886 / proteolysis
Similarity search - Function
Beta-Lactamase - #330 / Peptidoglycan D,D-transpeptidase FtsI / 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 ...Beta-Lactamase - #330 / Peptidoglycan D,D-transpeptidase FtsI / 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 / Beta-lactamase/transpeptidase-like / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-UE1 / Peptidoglycan D,D-transpeptidase FtsI / Peptidoglycan D,D-transpeptidase FtsI
Similarity search - Component
Biological speciesPseudomonas aeruginosa (unknown)
AuthorsHan, S. / Evdokimov, A.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2010
Title: Structural basis for effectiveness of siderophore-conjugated monocarbams against clinically relevant strains of Pseudomonas aeruginosa.
Authors: Han, S. / Zaniewski, R.P. / Marr, E.S. / Lacey, B.M. / Tomaras, A.P. / Evdokimov, A. / Miller, J.R. / Shanmugasundaram, V.
DepositionOct 20, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 22, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 8, 2012Group: Non-polymer description

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Deposited unit
A: Penicillin-binding protein 3
hetero molecules

Theoretical massNumber of molelcules
Total (without water)59,0452

  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)67.772, 83.768, 89.569
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121


#1: Protein Penicillin-binding protein 3

Mass: 58329.453 Da / Num. of mol.: 1 / Fragment: UNP Residues 50-579
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (unknown) / Strain: PAO1 / Gene: ftsI, PA4418, pbpB / Production host: Escherichia coli (E. coli) / References: UniProt: Q51504, UniProt: G3XD46*PLUS
#2: Chemical ChemComp-UE1 / (4S,7Z)-7-(2-amino-1,3-thiazol-4-yl)-1-[({4-[(2R)-2,3-dihydroxypropyl]-3-(4,5-dihydroxypyridin-2-yl)-5-oxo-4,5-dihydro-1H-1,2,4-triazol-1-yl}sulfonyl)amino]-4-formyl-10,10-dimethyl-1,6-dioxo-9-oxa-2,5,8-triazaundec-7-en-11-oate / MC-1 (open form)

Mass: 715.650 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C23H27N10O13S2
#3: Water ChemComp-HOH / water / Water

Mass: 18.015 Da / Num. of mol.: 539 / Source method: isolated from a natural source / Formula: H2O

Experimental details


ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

Sample preparation

CrystalDensity Matthews: 2.18 Å3/Da / Density % sol: 43.56 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 6.2
Details: 0.1M citrate, 30% PEG3350, 0.3M Mg(NO3)2, pH 6.2, VAPOR DIFFUSION, HANGING DROP

Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Aug 1, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.64→61.12 Å / Num. obs: 62097 / % possible obs: 99.1 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1


HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.641→61.12 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.95 / SU B: 1.788 / SU ML: 0.063 / Cross valid method: THROUGHOUT / ESU R: 0.097 / ESU R Free: 0.096 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20607 3153 5.1 %RANDOM
Rwork0.17351 ---
obs0.1752 58870 98.42 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 22.645 Å2
Baniso -1Baniso -2Baniso -3
1-0.74 Å20 Å20 Å2
2--0.25 Å20 Å2
3----0.99 Å2
Refinement stepCycle: LAST / Resolution: 1.641→61.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3822 0 48 539 4409
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0224106
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6981.9965609
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8185537
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.98123.081172
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.8615677
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.8541539
X-RAY DIFFRACTIONr_chiral_restr0.1160.2628
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0213154
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.2381.52545
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it3.40324118
X-RAY DIFFRACTIONr_scbond_it5.28131561
X-RAY DIFFRACTIONr_scangle_it8.2154.51472
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.641→1.684 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.326 158 -
Rwork0.246 3608 -
obs--82.05 %

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