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- PDB-5df9: CRYSTAL STRUCTURE OF PENICILLIN-BINDING PROTEIN 3 IN COMPLEX WITH... -

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Basic information

Entry
Database: PDB / ID: 5df9
TitleCRYSTAL STRUCTURE OF PENICILLIN-BINDING PROTEIN 3 IN COMPLEX WITH DEACYLATED PRODUCT OF CEFOPERAZONE
ComponentsCell division protein
KeywordsTRANSFERASE / cefoperazone / beta-lactam antibiotics / acyl-enzyme complex / de-acylation
Function / homology
Function and homology information


peptidoglycan glycosyltransferase activity / serine-type D-Ala-D-Ala carboxypeptidase / serine-type D-Ala-D-Ala carboxypeptidase activity / division septum assembly / FtsZ-dependent cytokinesis / penicillin binding / peptidoglycan biosynthetic process / cell wall organization / regulation of cell shape / proteolysis / plasma membrane
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 / 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 / Beta-lactamase / DD-peptidase/beta-lactamase superfamily / Beta-lactamase/transpeptidase-like / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-59J / Peptidoglycan D,D-transpeptidase FtsI
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsRen, J. / Nettleship, J.E. / Males, A. / Stuart, D.I. / Owens, R.J.
CitationJournal: Febs Lett. / Year: 2016
Title: Crystal structures of penicillin-binding protein 3 in complexes with azlocillin and cefoperazone in both acylated and deacylated forms.
Authors: Ren, J. / Nettleship, J.E. / Males, A. / Stuart, D.I. / Owens, R.J.
History
DepositionAug 26, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jan 13, 2016Provider: repository / Type: Initial release
Revision 1.1Feb 10, 2016Group: Database references
Revision 1.2Jan 10, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cell division protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,9865
Polymers61,1531
Non-polymers8344
Water37821
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area600 Å2
ΔGint-21 kcal/mol
Surface area23170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)176.884, 41.264, 87.786
Angle α, β, γ (deg.)90.00, 117.42, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Cell division protein / Penicillin-binding protein 3 / Pseudomonas aeruginosa genome assembly PAE221


Mass: 61152.590 Da / Num. of mol.: 1 / Fragment: UNP residues 35-579
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria)
Gene: pbpB, ftsI_2, ERS445055_04698, PAE221_03076, YQ19_27590
Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q51504, peptidoglycan glycosyltransferase
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-59J / (2R,5R)-2-[(R)-carboxy{[(2R)-2-{[(4-ethyl-2,3-dioxopiperazin-1-yl)carbonyl]amino}-2-(4-hydroxyphenyl)acetyl]amino}methyl]-5-methyl-5,6-dihydro-2H-1,3-thiazine-4-carboxylic acid


Mass: 549.554 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C23H27N5O9S
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 21 / 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: 2.33 Å3/Da / Density % sol: 47.1 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 9.5 / Details: 1.26 M (NH4)2SO4; 0.1 M CHES pH 9.5; 0.2 M NaCl

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9796 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jan 24, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9796 Å / Relative weight: 1
ReflectionResolution: 2.7→30 Å / Num. obs: 15866 / % possible obs: 100 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.092 / Net I/σ(I): 14.5
Reflection shellResolution: 2.7→2.8 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.722 / Mean I/σ(I) obs: 1.9 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.7.0032refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5DF8

5df8


Resolution: 2.7→29.97 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.931 / SU B: 31.791 / SU ML: 0.287 / Cross valid method: THROUGHOUT / ESU R Free: 0.352 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24927 786 5 %RANDOM
Rwork0.20236 ---
obs0.2046 15029 99.58 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 75.155 Å2
Baniso -1Baniso -2Baniso -3
1--4.43 Å20 Å21.75 Å2
2---3.26 Å20 Å2
3---4.41 Å2
Refinement stepCycle: 1 / Resolution: 2.7→29.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3886 0 54 21 3961
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.0194016
X-RAY DIFFRACTIONr_bond_other_d0.0010.023919
X-RAY DIFFRACTIONr_angle_refined_deg0.9031.9825451
X-RAY DIFFRACTIONr_angle_other_deg0.66938982
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.8585508
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.46923.136169
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.85715660
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.1521537
X-RAY DIFFRACTIONr_chiral_restr0.0490.2610
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0214570
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02907
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
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_it2.98713.3852035
X-RAY DIFFRACTIONr_mcbond_other2.97813.3852034
X-RAY DIFFRACTIONr_mcangle_it4.66722.5862542
X-RAY DIFFRACTIONr_mcangle_other4.66722.5882543
X-RAY DIFFRACTIONr_scbond_it3.66415.0591981
X-RAY DIFFRACTIONr_scbond_other3.66215.0581981
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.89224.8262910
X-RAY DIFFRACTIONr_long_range_B_refined8.33961.0744351
X-RAY DIFFRACTIONr_long_range_B_other8.33761.0694349
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.7→2.77 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.404 57 -
Rwork0.329 1110 -
obs--99.49 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
16.42552.2057-1.1870.8378-0.18940.85990.3758-0.0516-0.29080.165-0.0335-0.25830.0056-0.1295-0.34230.06420.0195-0.07230.1792-0.01780.50815.551618.8449-16.3232
22.65931.85841.38521.5441.11990.8501-0.0175-0.05130.20690.0241-0.02710.00670.05360.06330.04460.2375-0.03450.02960.27420.04660.1204-16.01349.9983-15.38
32.38460.40210.73370.83640.49990.550.030.1171-0.03870.006-0.16290.2832-0.03130.05880.13290.1858-0.0220.02950.1357-0.0450.2087-42.7221-4.0207-27.6867
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 150
2X-RAY DIFFRACTION2A151 - 265
3X-RAY DIFFRACTION3A266 - 561

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