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- PDB-4kqo: Crystal structure of penicillin-binding protein 3 from pseudomona... -

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Basic information

Entry
Database: PDB / ID: 4kqo
TitleCrystal structure of penicillin-binding protein 3 from pseudomonas aeruginosa in complex with piperacillin
ComponentsPenicillin-binding protein 3
KeywordsBiosynthetic Protein/Antibiotic / PENICILLIN-BINDING PROTEINS / PIPERACILLIN / CELL WALL BIOSYNTHESIS / TRANSPEPTIDASE / OUT PERIPLASMIC MEMBRANE / Biosynthetic Protein-Antibiotic complex
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 domain / Penicillin-binding protein, transpeptidase / 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 domain / Penicillin-binding protein, transpeptidase / 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
IMIDAZOLE / Piperacillin (Open Form) / Peptidoglycan D,D-transpeptidase FtsI
Similarity search - Component
Biological speciesPseudomonas aeruginosa (unknown)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.31 Å
AuthorsNettleship, J.E. / Stuart, D.I. / Owens, R.J. / Ren, J.
CitationJournal: Acs Chem.Biol. / Year: 2013
Title: Binding of (5S)-Penicilloic Acid to Penicillin Binding Protein 3.
Authors: van Berkel, S.S. / Nettleship, J.E. / Leung, I.K. / Brem, J. / Choi, H. / Stuart, D.I. / Claridge, T.D. / McDonough, M.A. / Owens, R.J. / Ren, J. / Schofield, C.J.
History
DepositionMay 15, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 6, 2013Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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)123,76110
Polymers122,3052
Non-polymers1,4558
Water4,972276
1
A: Penicillin-binding protein 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,8564
Polymers61,1531
Non-polymers7043
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Penicillin-binding protein 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,9046
Polymers61,1531
Non-polymers7525
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)57.049, 74.935, 82.785
Angle α, β, γ (deg.)71.26, 86.04, 85.59
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1010A58 - 562
2010B58 - 562

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Penicillin-binding protein 3


Mass: 61152.590 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (unknown) / Strain: PAO1 / Gene: ftsI, PA4418 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: G3XD46

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Non-polymers , 5 types, 284 molecules

#2: Chemical ChemComp-JPP / Piperacillin (Open Form)


Mass: 519.571 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C23H29N5O7S
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-IMD / IMIDAZOLE / Imidazole


Mass: 69.085 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H5N2
#5: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 276 / 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: 4

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Sample preparation

CrystalDensity Matthews: 2.73 Å3/Da / Density % sol: 54.93 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 2.5 M NaCl; 0.1 M imidazole, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.9173 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: May 30, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9173 Å / Relative weight: 1
ReflectionResolution: 2.31→50 Å / Num. obs: 55461 / % possible obs: 97.8 % / Observed criterion σ(I): -1.5 / Redundancy: 9.4 % / Rmerge(I) obs: 0.185 / Net I/σ(I): 6
Reflection shellResolution: 2.31→2.39 Å / Redundancy: 5.9 % / Rmerge(I) obs: 0.275 / Mean I/σ(I) obs: 1.5 / Num. unique all: 4929 / % possible all: 87.2

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Processing

Software
NameVersionClassification
MOLREPphasing
REFMAC5.7.0032refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3OCL
Resolution: 2.31→47.1 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.914 / SU B: 17.914 / SU ML: 0.21 / Cross valid method: THROUGHOUT / ESU R: 0.32 / ESU R Free: 0.231 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24965 2804 5.1 %RANDOM
Rwork0.21714 ---
obs0.2188 52657 97.81 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 42.412 Å2
Baniso -1Baniso -2Baniso -3
1-1.07 Å20.93 Å20.85 Å2
2--1.26 Å22.32 Å2
3----1.19 Å2
Refinement stepCycle: LAST / Resolution: 2.31→47.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7635 0 97 276 8008
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0197885
X-RAY DIFFRACTIONr_bond_other_d0.0030.027696
X-RAY DIFFRACTIONr_angle_refined_deg1.2711.98210705
X-RAY DIFFRACTIONr_angle_other_deg0.861317640
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.68551000
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.16723.222329
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.911151286
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.5051570
X-RAY DIFFRACTIONr_chiral_restr0.0660.21200
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0218979
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021779
Refine LS restraints NCS

Ens-ID: 1 / Number: 29717 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.08 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.31→2.37 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.42 184 -
Rwork0.357 3440 -
obs--86.2 %
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)
10.3237-0.2217-0.3150.3757-0.17371.0554-0.0204-0.0099-0.0282-0.0431-0.09420.00710.11490.16250.11460.0618-0.0075-0.01230.0724-0.00030.07320.26051.8389-2.2738
20.6511-0.3150.05840.2586-0.19760.965-0.0110.0479-0.01830.0554-0.01550.0672-0.0620.05860.02650.0489-0.02020.01610.06040.03130.062427.728217.94627.2224
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-10 - 9999
2X-RAY DIFFRACTION2B-10 - 9999

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