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

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Basic information

Entry
Database: PDB / ID: 3ocl
TitleCrystal structure of penicillin-binding protein 3 from Pseudomonas aeruginosa in complex with carbenicillin
ComponentsPenicillin-binding protein 3
KeywordsPENICILLIN-BINDING PROTEIN/ANTIBIOTIC / penicillin-binding proteins / Pseudomonas aeruginosa / carbenicillin / 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 / division septum assembly / serine-type D-Ala-D-Ala carboxypeptidase activity / 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-CB9 / Peptidoglycan D,D-transpeptidase FtsI
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 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
Revision 1.4Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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)61,6614
Polymers61,1531
Non-polymers5083
Water2,576143
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)69.475, 83.435, 89.845
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-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-CB9 / (2R,4S)-2-[(1R)-1-{[(2S)-2-carboxy-2-phenylacetyl]amino}-2-oxoethyl]-5,5-dimethyl-1,3-thiazolidine-4-carboxylic acid / Bound form of Carbenicillin


Mass: 380.416 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H20N2O6S
#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.: 143 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.13 Å3/Da / Density % sol: 42.23 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop
Details: 20%(w/v) polyethylene glycol 3350, 0.2M di-sodium tartrate, 0.5mM carbenicillin, VAPOR DIFFUSION, SITTING DROP, temperature 294K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8726 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Sep 5, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8726 Å / Relative weight: 1
ReflectionResolution: 2.3→30 Å / Num. obs: 24040 / % possible obs: 99.8 % / Observed criterion σ(I): -1.5 / Redundancy: 5.9 % / Rmerge(I) obs: 0.209 / Net I/σ(I): 7.8
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 5.6 % / Rmerge(I) obs: 0.872 / Mean I/σ(I) obs: 1.5 / Num. unique all: 2367 / % possible all: 99.9

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Processing

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

3equ


Resolution: 2.3→28.19 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.901 / SU B: 11.578 / SU ML: 0.135 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.365 / ESU R Free: 0.244 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.24794 1233 5.2 %RANDOM
Rwork0.20151 ---
obs0.20388 22550 99.84 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 26.268 Å2
Baniso -1Baniso -2Baniso -3
1-0.28 Å20 Å20 Å2
2--1.92 Å20 Å2
3----2.2 Å2
Refinement stepCycle: LAST / Resolution: 2.3→28.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3801 0 33 143 3977
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0223908
X-RAY DIFFRACTIONr_bond_other_d0.0010.022690
X-RAY DIFFRACTIONr_angle_refined_deg1.1271.9775304
X-RAY DIFFRACTIONr_angle_other_deg0.85236533
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.355495
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.40223.193166
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.59815642
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.3351536
X-RAY DIFFRACTIONr_chiral_restr0.0650.2598
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0214368
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02784
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.3→2.359 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.313 93 -
Rwork0.27 1624 -
obs--99.83 %
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)
10.60850.68460.52960.86640.98252.11630.0502-0.0853-0.00030.0027-0.06670.0144-0.2780.03560.01660.14720.0172-0.00970.121-0.02090.05738.912836.62220.7101
21.7685-0.93861.18652.7719-2.31713.4192-0.00640.1384-0.1283-0.3025-0.15770.0005-0.14120.12650.16410.2094-0.0479-0.03110.0979-0.0230.041710.451828.21942.2356
30.68760.66050.17472.21960.84340.6310.0364-0.00450.0131-0.02170.10990.03230.17240.0189-0.14630.1367-0.0325-0.07860.0494-0.00660.11058.01864.6155-29.7331
40.3969-0.0540.12190.22480.47021.5157-0.0223-0.0563-0.0027-0.00810.04610.01970.0729-0.0226-0.02390.0488-0.0405-0.00720.05190.010.08943.455618.1452-10.1605
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A53 - 78
2X-RAY DIFFRACTION1A151 - 221
3X-RAY DIFFRACTION2A79 - 150
4X-RAY DIFFRACTION3A308 - 360
5X-RAY DIFFRACTION4A222 - 307
6X-RAY DIFFRACTION4A361 - 559
7X-RAY DIFFRACTION4A1

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