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- PDB-3ocn: Crystal structure of penicillin-binding protein 3 from Pseudomona... -

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Basic information

Entry
Database: PDB / ID: 3ocn
TitleCrystal structure of penicillin-binding protein 3 from Pseudomonas aeruginosa in complex with ceftazidime
Componentspenicillin-binding protein 3
KeywordsPENICILLIN-BINDING PROTEIN/ANTIBIOTIC / penicillin-binding proteins / Pseudomonas aeruginosa / ceftazidime / Structural Genomics / Oxford Protein Production Facility / OPPF / transpeptidase / cell wall biosynthesis / out periplasmic membrane / PENICILLIN-BINDING PROTEIN-ANTIBIOTIC complex
Function / homology
Function and homology information


peptidoglycan glycosyltransferase activity / serine-type D-Ala-D-Ala carboxypeptidase / FtsZ-dependent cytokinesis / serine-type D-Ala-D-Ala carboxypeptidase activity / division septum assembly / 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 / DD-peptidase/beta-lactamase superfamily ...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-CTJ / Peptidoglycan D,D-transpeptidase FtsI
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.61 Å
AuthorsSainsbury, S. / Bird, L. / Stuart, D.I. / Owens, R.J. / Ren, J. / Oxford Protein Production Facility (OPPF)
CitationJournal: J.Mol.Biol. / Year: 2011
Title: Crystal structures of penicillin-binding protein 3 from Pseudomonas aeruginosa: comparison of native and antibiotic-bound forms
Authors: Sainsbury, S. / Bird, L. / Rao, V. / Shepherd, S.M. / Stuart, D.I. / Hunter, W.N. / Owens, R.J. / Ren, J.
History
DepositionAug 10, 2010Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 10, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 26, 2014Group: Database references
Revision 1.3Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: penicillin-binding protein 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,7022
Polymers61,1531
Non-polymers5501
Water68538
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)67.081, 81.812, 87.789
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein penicillin-binding protein 3


Mass: 61152.590 Da / Num. of mol.: 1 / Fragment: residues in UNP 35-579
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Strain: PAO1 / Gene: PA4418 / Plasmid: OPPF6502 / Production host: Escherichia coli (E. coli) / Strain (production host): DE3 / References: UniProt: Q51504
#2: Chemical ChemComp-CTJ / 1-({(2R)-2-[(1R)-1-{[(2Z)-2-(2-amino-1,3-thiazol-4-yl)-2-{[(2-carboxypropan-2-yl)oxy]imino}acetyl]amino}-2-oxoethyl]-4-carboxy-3,6-dihydro-2H-1,3-thiazin-5-yl}methyl)pyridinium


Mass: 549.600 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C22H25N6O7S2
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 38 / 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: 1.97 Å3/Da / Density % sol: 37.55 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 7.8
Details: 25%(w/v) polyethylene glycol 3350, 0.1M Bis-Tris propane, 1%(w/v) protamine sulphate, pH 7.8, VAPOR DIFFUSION, SITTING DROP, temperature 294K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.975 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 7, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.975 Å / Relative weight: 1
ReflectionResolution: 2.6→30 Å / Num. obs: 15047 / % possible obs: 98.6 % / Observed criterion σ(I): -1.5 / Redundancy: 5.6 % / Rmerge(I) obs: 0.166 / Net I/σ(I): 11.9
Reflection shellResolution: 2.6→2.69 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.545 / Mean I/σ(I) obs: 2.5 / Num. unique all: 1331 / % possible all: 89.3

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Processing

Software
NameClassification
REFMACrefinement
HKL-2000data reduction
SCALEPACKdata scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3OCL

3ocl


Resolution: 2.61→29.85 Å / Cor.coef. Fo:Fc: 0.926 / Cor.coef. Fo:Fc free: 0.891 / SU B: 20.68 / SU ML: 0.202 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.369 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.26264 746 5 %RANDOM
Rwork0.20587 ---
obs0.20865 14178 97.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 32.262 Å2
Baniso -1Baniso -2Baniso -3
1-3.88 Å20 Å20 Å2
2---0.85 Å20 Å2
3----3.03 Å2
Refinement stepCycle: LAST / Resolution: 2.61→29.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3841 0 31 38 3910
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0223948
X-RAY DIFFRACTIONr_bond_other_d0.0010.022711
X-RAY DIFFRACTIONr_angle_refined_deg1.0191.9775359
X-RAY DIFFRACTIONr_angle_other_deg0.78236582
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4015501
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.40423.155168
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.06315653
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.4211537
X-RAY DIFFRACTIONr_chiral_restr0.0560.2601
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0214433
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02795
LS refinement shellResolution: 2.607→2.674 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.435 40 -
Rwork0.302 886 -
obs--83.57 %
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)
11.09371.24131.76691.50582.24953.87790.01650.0343-0.02710.09580.0678-0.0572-0.03080.1656-0.08430.2158-0.0164-0.02910.1568-0.0160.10218.08835.64921.375
22.6219-2.17941.13785.5543-1.85526.077-0.1550.34210.02690.0407-0.1399-0.054-0.3130.46260.29490.2951-0.12650.00180.11780.01950.01689.32427.24641.529
31.0981.1401-0.35323.86532.09933.0566-0.07970.0226-0.0702-0.09190.126-0.24830.3765-0.0595-0.04630.2115-0.05770.02360.11270.00830.13358.8453.031-29.03
40.8525-0.2236-0.30970.6907-0.00991.3578-0.0402-0.1001-0.0272-0.05790.03580.02490.07970.05330.00440.0592-0.0139-0.00010.1-0.00340.12142.77716.165-9.705
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A50 - 78
2X-RAY DIFFRACTION1A151 - 221
3X-RAY DIFFRACTION2A79 - 150
4X-RAY DIFFRACTION3A308 - 360
5X-RAY DIFFRACTION4A222 - 307
6X-RAY DIFFRACTION4A361 - 558
7X-RAY DIFFRACTION4A1

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