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- PDB-5j8x: CRYSTAL STRUCTURE OF E. COLI PBP5 WITH 2C -

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Basic information

Entry
Database: PDB / ID: 5j8x
TitleCRYSTAL STRUCTURE OF E. COLI PBP5 WITH 2C
ComponentsD-alanyl-D-alanine carboxypeptidase DacA
KeywordsHYDROLASE / antibiotic resistance / penicillin binding protein / boronic acid
Function / homology
Function and homology information


peptidoglycan metabolic process / serine-type D-Ala-D-Ala carboxypeptidase / serine-type D-Ala-D-Ala carboxypeptidase activity / penicillin binding / peptidoglycan biosynthetic process / carboxypeptidase activity / cell wall organization / beta-lactamase activity / beta-lactamase / regulation of cell shape ...peptidoglycan metabolic process / serine-type D-Ala-D-Ala carboxypeptidase / serine-type D-Ala-D-Ala carboxypeptidase activity / penicillin binding / peptidoglycan biosynthetic process / carboxypeptidase activity / cell wall organization / beta-lactamase activity / beta-lactamase / regulation of cell shape / outer membrane-bounded periplasmic space / protein homodimerization activity / proteolysis / plasma membrane
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
Chem-OK3 / D-alanyl-D-alanine carboxypeptidase DacA
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.53 Å
AuthorsBrem, J. / Cain, R. / McDonough, M.A. / Clifton, I.J. / Fishwick, C.W.G. / Schofield, C.J.
CitationJournal: Nat Commun / Year: 2016
Title: Structural basis of metallo-beta-lactamase, serine-beta-lactamase and penicillin-binding protein inhibition by cyclic boronates.
Authors: Brem, J. / Cain, R. / Cahill, S. / McDonough, M.A. / Clifton, I.J. / Jimenez-Castellanos, J.C. / Avison, M.B. / Spencer, J. / Fishwick, C.W. / Schofield, C.J.
History
DepositionApr 8, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0Aug 17, 2016Provider: repository / Type: Initial release
Revision 2.0Oct 30, 2019Group: Data collection / Derived calculations ...Data collection / Derived calculations / Non-polymer description / Structure summary
Category: chem_comp / entity / pdbx_entity_nonpoly
Item: _chem_comp.formula / _chem_comp.name ..._chem_comp.formula / _chem_comp.name / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Revision 2.1Jan 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: D-alanyl-D-alanine carboxypeptidase DacA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,8402
Polymers42,4831
Non-polymers3571
Water48627
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area15730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.223, 61.606, 138.430
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP22121

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Components

#1: Protein D-alanyl-D-alanine carboxypeptidase DacA / DD-peptidase / Beta-lactamase / Penicillin-binding protein 5 / PBP-5


Mass: 42483.160 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: dacA, pfv, b0632, JW0627 / Plasmid: pdacA Nhis / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: P0AEB2, serine-type D-Ala-D-Ala carboxypeptidase, beta-lactamase
#2: Chemical ChemComp-OK3 / (4~{R})-4-[[4-(aminomethyl)phenyl]carbonylamino]-3,3-bis(oxidanyl)-2-oxa-3-boranuidabicyclo[4.4.0]deca-1(10),6,8-triene-10-carboxylic acid


Mass: 357.146 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H18BN2O6
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 27 / 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: 2.52 Å3/Da / Density % sol: 51.2 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 0.1 M Hepes pH 7.5, 10% 2-Propanol, 20% PEG 4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Feb 22, 2016 / Details: MIRRORS
RadiationMonochromator: DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.53→28.497 Å / Num. obs: 14992 / % possible obs: 99.5 % / Observed criterion σ(I): -3 / Redundancy: 6.4 % / Biso Wilson estimate: 46.34 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.098 / Net I/σ(I): 13.5
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
2.53-2.680.5931.79197.6
2.68-2.860.4042.82199.7
2.86-3.090.2524.64199.9
3.09-3.380.1656.96199.7
3.38-3.770.09612.46199
3.77-4.340.06617.82198.8
4.34-5.290.05620.35198.1
5.29-7.350.05720.84199.3
7.35-28.4970.03828.68197.3

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation5.97 Å28.5 Å
Translation5.97 Å28.5 Å

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACT3.2data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1NZO

1nzo


Resolution: 2.53→28.497 Å / SU ML: 0.3 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 21.18
RfactorNum. reflection% reflection
Rfree0.2333 1496 10 %
Rwork0.2 --
obs0.2033 14959 99.5 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 119.06 Å2 / Biso mean: 54.1937 Å2 / Biso min: 27.63 Å2
Refinement stepCycle: final / Resolution: 2.53→28.497 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2546 0 25 27 2598
Biso mean--46.52 51.58 -
Num. residues----340
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0032620
X-RAY DIFFRACTIONf_angle_d0.5553558
X-RAY DIFFRACTIONf_chiral_restr0.041400
X-RAY DIFFRACTIONf_plane_restr0.003468
X-RAY DIFFRACTIONf_dihedral_angle_d14.4361545
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 11

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.53-2.60740.33911290.29041163129297
2.6074-2.70050.29881340.259611981332100
2.7005-2.80860.26851350.250812291364100
2.8086-2.93630.28991330.235711921325100
2.9363-3.09090.27291360.233612181354100
3.0909-3.28430.26851320.234311991331100
3.2843-3.53740.22331350.213712161351100
3.5374-3.89260.19711380.18512321370100
3.8926-4.4540.20621370.162112401377100
4.454-5.60460.19811400.168312551395100
5.6046-28.49880.23421470.189113211468100
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)
15.82440.3015-0.91412.0391-0.40673.525-0.06270.7402-0.509-0.1113-0.032-0.12460.07550.16830.070.28410.0560.00730.3159-0.07170.267226.11757.1185291.8553
26.4657-0.7718-0.57464.4427-2.15259.77170.0738-0.44160.1979-0.0761-0.30270.41850.0579-1.10610.19720.39470.1059-0.03770.8517-0.01220.5377-0.095216.9629302.7943
36.3454-0.4076-1.33911.4668-0.46323.9624-0.03140.6168-0.4112-0.0052-0.03470.25130.1467-0.64640.08650.3166-0.0167-0.01370.3909-0.06460.360510.9587.6548294.3877
45.3619-0.3867-0.67013.75340.97594.66840.0847-0.13390.2066-0.04040.00480.0544-0.10110.0414-0.12280.27740.0149-0.0150.25140.00760.278922.855415.0632301.4103
58.46360.8967-3.13233.5469-0.47496.78380.0298-0.1925-0.67140.0981-0.3004-0.6574-0.50281.42560.06460.3871-0.0283-0.04820.4504-0.06040.326536.610212.7516295.2966
61.0919-1.42382.5404-0.0573-1.32925.6203-0.1824-0.0451-0.01450.37170.1240.2432-1.23690.45620.14230.8398-0.09860.04760.57070.02610.477832.635121.8112262.2344
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 4 through 60 )A4 - 60
2X-RAY DIFFRACTION2chain 'A' and (resid 61 through 95 )A61 - 95
3X-RAY DIFFRACTION3chain 'A' and (resid 96 through 175 )A96 - 175
4X-RAY DIFFRACTION4chain 'A' and (resid 176 through 246 )A176 - 246
5X-RAY DIFFRACTION5chain 'A' and (resid 247 through 266 )A247 - 266
6X-RAY DIFFRACTION6chain 'A' and (resid 267 through 358 )A267 - 358

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