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- PDB-5df7: CRYSTAL STRUCTURE OF PENICILLIN-BINDING PROTEIN 3 FROM PSEUDOMONA... -

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Basic information

Entry
Database: PDB / ID: 5df7
TitleCRYSTAL STRUCTURE OF PENICILLIN-BINDING PROTEIN 3 FROM PSEUDOMONAS AERUGINOSA IN COMPLEX WITH AZLOCILLIN
ComponentsCell division protein
KeywordsTRANSFERASE / azlocillin / 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-59H / IMIDAZOLE / Peptidoglycan D,D-transpeptidase FtsI
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 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 1.1Jan 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
Revision 1.2Oct 1, 2025Group: Advisory / Derived calculations / Structure summary
Category: pdbx_entry_details / pdbx_validate_close_contact / struct_conn

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cell division protein
B: Cell division protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)123,78813
Polymers122,3052
Non-polymers1,48311
Water6,882382
1
A: Cell division protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,8135
Polymers61,1531
Non-polymers6604
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Cell division protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,9768
Polymers61,1531
Non-polymers8237
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)57.253, 74.919, 82.722
Angle α, β, γ (deg.)71.26, 85.99, 85.69
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
1114A1 - 900
2114B1 - 900

NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(0.99999, 0.003826, 0.002147), (0.003822, -0.999991, 0.001942), (0.002155, -0.001934, -0.999996)-28.73258, 19.4649, 7.46004

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Components

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Protein , 1 types, 2 molecules AB

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


Mass: 61152.590 Da / Num. of mol.: 2
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

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Non-polymers , 5 types, 393 molecules

#2: Chemical ChemComp-59H / (2R,4S)-5,5-dimethyl-2-[(1R)-2-oxo-1-{[(2R)-2-{[(2-oxoimidazolidin-1-yl)carbonyl]amino}-2-phenylacetyl]amino}ethyl]-1,3-thiazolidine-4-carboxylic acid


Mass: 463.507 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C20H25N5O6S
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-IMD / IMIDAZOLE


Mass: 69.085 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H5N2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 382 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.74 Å3/Da / Density % sol: 55.05 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: 2.5 M NaCl; 0.1 M imidazole pH 8.0

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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→50 Å / Num. obs: 76005 / % possible obs: 86.7 % / Redundancy: 2.7 % / Rmerge(I) obs: 0.137 / Net I/σ(I): 7.4
Reflection shellResolution: 2→2.07 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.579 / Mean I/σ(I) obs: 1.6 / % possible all: 78.3

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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: 4KQO

4kqo


Resolution: 2→47.19 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.931 / SU B: 9.276 / SU ML: 0.125 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.191 / ESU R Free: 0.169 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.23656 3803 5 %RANDOM
Rwork0.19752 ---
obs0.19946 72149 86.68 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 40.265 Å2
Baniso -1Baniso -2Baniso -3
1-0.15 Å20.62 Å20.8 Å2
2--0.7 Å21.28 Å2
3----0.28 Å2
Refinement stepCycle: 1 / Resolution: 2→47.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7649 0 96 382 8127
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0197896
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.0741.98110716
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.29951002
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.58623.182330
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.963151288
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.4831571
X-RAY DIFFRACTIONr_chiral_restr0.0720.21201
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0216015
X-RAY DIFFRACTIONr_gen_planes_other
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_it3.5868.3614023
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it5.09714.0495020
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it4.8649.8253873
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined9.13239.32312120
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 3722 / Refine-ID: X-RAY DIFFRACTION

TypeRms dev position (Å)Weight position
medium positional0.320
medium thermal5.472
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.334 228 -
Rwork0.322 4792 -
obs--77.42 %
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)
10.1915-0.1463-0.23460.2398-0.05410.7149-0.01580.02360-0.0028-0.0249-0.02050.0505-0.0210.04070.02210.0003-0.00180.0161-0.00640.01580.03571.8041-2.0367
20.6292-0.10250.06910.0841-0.19380.7139-0.01420.04530.02960.0294-0.01190.0016-0.04190.0140.02610.02570.00780.0090.02640.01210.018327.846117.97427.1781
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A50 - 564
2X-RAY DIFFRACTION2B57 - 563

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