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- PDB-3oc2: Crystal structure of penicillin-binding protein 3 from Pseudomona... -

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Basic information

Entry
Database: PDB / ID: 3oc2
TitleCrystal structure of penicillin-binding protein 3 from Pseudomonas aeruginosa
ComponentsPenicillin-binding protein 3
KeywordsPENICILLIN-BINDING PROTEIN / penicillin-binding proteins / Pseudomonas aeruginosa / Structural Genomics / Oxford Protein Production Facility / OPPF / transpeptidase / cell wall biosynthesis / out periplasmic membrane
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 / proteolysis / plasma membrane
Similarity search - Function
Beta-Lactamase - #330 / Penicillin-binding protein 2a (Domain 2) / Penicillin-binding protein 2a (Domain 2) / 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 - #330 / Penicillin-binding protein 2a (Domain 2) / Penicillin-binding protein 2a (Domain 2) / 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 / Alpha-Beta Complex / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Peptidoglycan D,D-transpeptidase FtsI
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.968 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 9, 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 1.3Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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_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)61,2594
Polymers61,1531
Non-polymers1063
Water3,909217
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)66.761, 81.514, 85.937
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
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 / Chloride


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 217 / 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: 1.91 Å3/Da / Density % sol: 35.66 %
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: I04 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 25, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.968→30 Å / Num. obs: 32803 / % possible obs: 99.6 % / Observed criterion σ(I): -1.5 / Redundancy: 10.4 % / Biso Wilson estimate: 23.92 Å2 / Rmerge(I) obs: 0.143 / Net I/σ(I): 23.9
Reflection shellResolution: 2→2.07 Å / Redundancy: 5.7 % / Rmerge(I) obs: 0.575 / Mean I/σ(I) obs: 3 / Num. unique all: 3150 / % possible all: 96.7

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Processing

Software
NameVersionClassification
PHENIXmodel building
PHENIX(phenix.refine: 1.6.1_353)refinement
HKL-2000data reduction
SCALEPACKdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.968→29.07 Å / SU ML: 0.23 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2111 1649 5.04 %RANDOM
Rwork0.168 ---
obs0.1702 32749 96.58 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 60.838 Å2 / ksol: 0.389 e/Å3
Displacement parametersBiso mean: 32.8796 Å2
Baniso -1Baniso -2Baniso -3
1-5.9743 Å2-0 Å2-0 Å2
2---3.8921 Å2-0 Å2
3----2.0822 Å2
Refinement stepCycle: LAST / Resolution: 1.968→29.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3781 0 3 217 4001
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073853
X-RAY DIFFRACTIONf_angle_d1.1075225
X-RAY DIFFRACTIONf_chiral_restr0.075590
X-RAY DIFFRACTIONf_plane_restr0.005687
X-RAY DIFFRACTIONf_dihedral_angle_d14.1071440
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.9685-2.03880.28391160.23492106222266
2.0388-2.12040.24191730.19443135330899
2.1204-2.21690.21891800.17731633343100
2.2169-2.33370.22361660.165331793345100
2.3337-2.47990.22481650.165132053370100
2.4799-2.67120.23991630.161432043367100
2.6712-2.93980.20221560.160732143370100
2.9398-3.36470.18631720.152332263398100
3.3647-4.23710.18151670.142832833450100
4.2371-29.07290.21061910.184233853576100
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)
10.16870.53321.4937-0.03760.43221.825-0.1206-0.03670.04710.0492-0.0766-0.1874-0.32470.17790.12810.2013-0.0617-0.06920.2653-0.00550.2258.120235.126920.6907
20.28660.05410.12981.11970.07590.7953-0.21310.16330.0745-0.7850.05670.0693-0.26990.05080.12770.5359-0.0438-0.05980.19430.02380.18558.814727.564240.9161
30.8308-0.3747-0.48820.73520.39641.42740.0038-0.0316-0.08240.0603-0.02250.0343-0.00330.00710.01960.087-0.0157-0.00820.08090.00090.11133.088416.6491-9.7733
40.2210.24490.06930.28150.26171.0199-0.0632-0.05610.01920.01670.02660.10680.2651-0.11210.06470.21170.00190.02130.1291-0.04020.14379.0922.993-28.6634
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain A and (resid 50:78 or resid 151:221)A50 - 78
2X-RAY DIFFRACTION1chain A and (resid 50:78 or resid 151:221)A151 - 221
3X-RAY DIFFRACTION2chain A and resid 79:150A79 - 150
4X-RAY DIFFRACTION3chain A and (resid 222:307 or resid 361:558)A222 - 307
5X-RAY DIFFRACTION3chain A and (resid 222:307 or resid 361:558)A361 - 558
6X-RAY DIFFRACTION4chain A and resid 308:360A308 - 360

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