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- PDB-4k91: Crystal structure of Penicillin-Binding Protein 5 (PBP5) from Pse... -

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Basic information

Entry
Database: PDB / ID: 4k91
TitleCrystal structure of Penicillin-Binding Protein 5 (PBP5) from Pseudomonas aeruginosa in apo state
ComponentsD-ala-D-ala-carboxypeptidase
KeywordsHYDROLASE / DD-carboxypeptidase / membrane associated
Function / homology
Function and homology information


serine-type D-Ala-D-Ala carboxypeptidase / serine-type D-Ala-D-Ala carboxypeptidase activity / peptidoglycan biosynthetic process
Similarity search - Function
Peptidoglycan synthesis regulatory factor (PBP3), Domain 2 / D-Ala-D-Ala carboxypeptidase, C-terminal domain / D-Ala-D-Ala carboxypeptidase, C-terminal domain superfamily / Peptidase S11, D-Ala-D-Ala carboxypeptidase A, C-terminal / Penicillin-binding protein 5, C-terminal domain / Penicillin-binding protein 5, C-terminal domain / Penicillin-binding protein, C-terminal domain superfamily / Peptidase S11, D-alanyl-D-alanine carboxypeptidase A, N-terminal / Peptidase S11, D-alanyl-D-alanine carboxypeptidase A / D-alanyl-D-alanine carboxypeptidase ...Peptidoglycan synthesis regulatory factor (PBP3), Domain 2 / D-Ala-D-Ala carboxypeptidase, C-terminal domain / D-Ala-D-Ala carboxypeptidase, C-terminal domain superfamily / Peptidase S11, D-Ala-D-Ala carboxypeptidase A, C-terminal / Penicillin-binding protein 5, C-terminal domain / Penicillin-binding protein 5, C-terminal domain / Penicillin-binding protein, C-terminal domain superfamily / Peptidase S11, D-alanyl-D-alanine carboxypeptidase A, N-terminal / Peptidase S11, D-alanyl-D-alanine carboxypeptidase A / D-alanyl-D-alanine carboxypeptidase / Beta-lactamase / DD-peptidase/beta-lactamase superfamily / Beta-lactamase/transpeptidase-like / Sandwich / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
SUCCINIC ACID / Serine-type D-Ala-D-Ala carboxypeptidase / Serine-type D-Ala-D-Ala carboxypeptidase
Similarity search - Component
Biological speciesPseudomonas aeruginosa UCBPP-PA14 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.05 Å
AuthorsSmith, J. / Toth, M. / Vakulenko, S. / Mobashery, S. / Chen, Y.
CitationJournal: Antimicrob.Agents Chemother. / Year: 2013
Title: Structural analysis of the role of Pseudomonas aeruginosa penicillin-binding protein 5 in beta-lactam resistance.
Authors: Smith, J.D. / Kumarasiri, M. / Zhang, W. / Hesek, D. / Lee, M. / Toth, M. / Vakulenko, S. / Fisher, J.F. / Mobashery, S. / Chen, Y.
History
DepositionApr 19, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 25, 2013Provider: repository / Type: Initial release
Revision 1.1Feb 28, 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: D-ala-D-ala-carboxypeptidase
B: D-ala-D-ala-carboxypeptidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,9845
Polymers75,6302
Non-polymers3543
Water2,792155
1
A: D-ala-D-ala-carboxypeptidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,9332
Polymers37,8151
Non-polymers1181
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: D-ala-D-ala-carboxypeptidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,0513
Polymers37,8151
Non-polymers2362
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)232.143, 39.909, 85.461
Angle α, β, γ (deg.)90.000, 111.030, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein D-ala-D-ala-carboxypeptidase


Mass: 37814.934 Da / Num. of mol.: 2
Fragment: A soluble fragment excluding the 24-residue N-terminal signal peptide and the 17-residue C-terminal membrane anchor (unp residues 25-369)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa UCBPP-PA14 (bacteria)
Strain: PAO1 / Gene: dacC, PA14_12100 / Plasmid: pET24d(+) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q02SG6, UniProt: A0A0H2ZFH3*PLUS, serine-type D-Ala-D-Ala carboxypeptidase
#2: Chemical ChemComp-SIN / SUCCINIC ACID / Succinic acid


Mass: 118.088 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H6O4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 155 / 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: 2.44 Å3/Da / Density % sol: 49.65 %
Crystal growTemperature: 288 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 20% PEG 3350, 0.2 M succinic acid, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 288K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.11587 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 3, 2011 / Details: mirrors
RadiationMonochromator: DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.11587 Å / Relative weight: 1
ReflectionResolution: 2.05→50 Å / Num. all: 46573 / Num. obs: 46480 / % possible obs: 99.8 % / Observed criterion σ(I): 3 / Redundancy: 3.8 % / Rmerge(I) obs: 0.067 / Χ2: 1.069 / Net I/σ(I): 13.2
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.05-2.093.70.61323141.052199.6
2.09-2.123.80.54522591.0421100
2.12-2.163.70.44222971.041199.9
2.16-2.213.80.4123271.052199.6
2.21-2.263.80.36522831.151100
2.26-2.313.80.31323091.024199.8
2.31-2.373.80.26523211.063199.9
2.37-2.433.90.23722991.034199.9
2.43-2.53.90.1923161.0241100
2.5-2.583.90.16123060.988199.9
2.58-2.683.90.13823381.1731100
2.68-2.783.90.12423071.112199.8
2.78-2.913.80.10822891.0541100
2.91-3.063.80.09123761.171199.9
3.06-3.253.70.07922961.07199.9
3.25-3.513.60.06823351.109199.9
3.51-3.863.60.06123341.088199.7
3.86-4.423.60.05423621.035199.7
4.42-5.563.70.04623601.143199.1
5.56-503.80.03224520.967199

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACT3.11data extraction
HKL-2000data collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.05→39.89 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.934 / WRfactor Rfree: 0.2926 / WRfactor Rwork: 0.2324 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.7923 / SU B: 5.646 / SU ML: 0.153 / SU R Cruickshank DPI: 0.2193 / SU Rfree: 0.1933 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.219 / ESU R Free: 0.193 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2629 2344 5.1 %RANDOM
Rwork0.2121 ---
obs0.2147 46302 99.26 %-
all-46647 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 118.72 Å2 / Biso mean: 55.0341 Å2 / Biso min: 21.05 Å2
Baniso -1Baniso -2Baniso -3
1-0.35 Å20 Å2-0.49 Å2
2--0.72 Å20 Å2
3----1.42 Å2
Refinement stepCycle: LAST / Resolution: 2.05→39.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5239 0 24 155 5418
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0225369
X-RAY DIFFRACTIONr_angle_refined_deg1.2871.9627260
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.7215686
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.87624.937237
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.00315939
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.8791530
X-RAY DIFFRACTIONr_chiral_restr0.110.2815
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0214048
X-RAY DIFFRACTIONr_mcbond_it1.411.53397
X-RAY DIFFRACTIONr_mcangle_it2.33425437
X-RAY DIFFRACTIONr_scbond_it3.47531972
X-RAY DIFFRACTIONr_scangle_it5.4584.51823
LS refinement shellResolution: 2.05→2.103 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.352 175 -
Rwork0.3 3176 -
all-3351 -
obs--97.41 %

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