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- PDB-1z6f: Crystal structure of penicillin-binding protein 5 from E. coli in... -

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Basic information

Entry
Database: PDB / ID: 1z6f
TitleCrystal structure of penicillin-binding protein 5 from E. coli in complex with a boronic acid inhibitor
ComponentsPenicillin-binding protein 5
KeywordsHYDROLASE / peptidoglycan synthesis / penicillin-binding protein / dd-carboxypeptidase / 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-BO9 / D-alanyl-D-alanine carboxypeptidase DacA / D-alanyl-D-alanine carboxypeptidase DacA
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIMPLE REFINEMENT / Resolution: 1.6 Å
AuthorsNicola, G. / Peddi, S. / Stefanova, M. / Nicholas, R.A. / Gutheil, W.G. / Davies, C.
CitationJournal: Biochemistry / Year: 2005
Title: Crystal Structure of Escherichia coli Penicillin-Binding Protein 5 Bound to a Tripeptide Boronic Acid Inhibitor: A Role for Ser-110 in Deacylation.
Authors: Nicola, G. / Peddi, S. / Stefanova, M. / Nicholas, R.A. / Gutheil, W.G. / Davies, C.
History
DepositionMar 22, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 21, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Oct 11, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software / Item: _software.classification / _software.name
Revision 1.4Aug 23, 2023Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms / struct_conn / 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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 999SEQUENCE TO PRODUCE SPBP 5, THE LAST 17 AMINO ACIDS WERE REMOVED BY DELETION OF THEIR RESPECTIVE ...SEQUENCE TO PRODUCE SPBP 5, THE LAST 17 AMINO ACIDS WERE REMOVED BY DELETION OF THEIR RESPECTIVE CODONS, AN ADDITIONAL SIX AMINO ACIDS (GDPVID) WERE INTRODUCED AT THE C TERMINUS DUE TO READ-THROUGH TO THE STOP CODON. NONE OF THESE NON-NATIVE RESIDUES ARE VISIBLE IN THE ELECTRON DENSITY MAP. THE FIRST 29 AMINO ACIDS OF THE PROTEIN ENCODED BY THE OPEN READING FRAME REPRESENT THE SIGNAL SEQUENCE, WHICH IS REMOVED DURING MATURATION AND TRANSPORT TO THE PERIPLASMIC SPACE AND IS NOT PRESENT IN THIS CONSTRUCT.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Penicillin-binding protein 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,5143
Polymers39,8411
Non-polymers6732
Water6,323351
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)109.760, 50.250, 84.310
Angle α, β, γ (deg.)90.00, 120.20, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Penicillin-binding protein 5 / D-alanyl-D-alanine carboxypeptidase fraction A / DD-peptidase / DD-carboxypeptidase / PBP-5


Mass: 39841.117 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: dacA, pfv / Plasmid: PBR322 / Production host: Escherichia coli (E. coli) / Strain (production host): MC1061
References: UniProt: P04287, UniProt: P0AEB2*PLUS, serine-type D-Ala-D-Ala carboxypeptidase
#2: Chemical ChemComp-BO9 / N1-[(1R)-1-(DIHYDROXYBORYL)ETHYL]-N2-[(TERT-BUTOXYCARBONYL)-D-GAMMA-GLUTAMYL]-N6-[(BENZYLOXY)CARBONYL-L-LYSINAMIDE / BOC-GAMMA-D-GLU-L-LYS(CBZ)-D-BOROALA


Mass: 580.436 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C26H41BN4O10
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 351 / 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: 2.9 Å3/Da / Density % sol: 57 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 100mM Tris, 8% PEG 400, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 294K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Mar 24, 2004
RadiationMonochromator: Double crystal monochromator Si-220 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.6→30 Å / Num. all: 52064 / Num. obs: 52064 / % possible obs: 98.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.4 % / Biso Wilson estimate: 21.5 Å2 / Rmerge(I) obs: 0.065 / Net I/σ(I): 24.4
Reflection shellResolution: 1.6→1.66 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.466 / Mean I/σ(I) obs: 2.4 / Num. unique all: 5239 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
MAR345data collection
SCALEPACKdata scaling
RefinementMethod to determine structure: SIMPLE REFINEMENT
Starting model: PDB entry 1NZO

1nzo


Resolution: 1.6→30 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.94 / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.101 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.24 2555 5 %RANDOM
Rwork0.213 ---
all0.215 51268 --
obs0.215 51268 98.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 21.342 Å2
Baniso -1Baniso -2Baniso -3
1-0.43 Å20 Å2-0.19 Å2
2---1 Å20 Å2
3---0.38 Å2
Refinement stepCycle: LAST / Resolution: 1.6→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2732 0 47 351 3130
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0222890
X-RAY DIFFRACTIONr_angle_refined_deg1.3551.9723902
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8065359
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.24225.188133
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.60615503
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.5321515
X-RAY DIFFRACTIONr_chiral_restr0.0910.2431
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022186
X-RAY DIFFRACTIONr_nbd_refined0.1980.21397
X-RAY DIFFRACTIONr_nbtor_refined0.3060.22006
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1350.2310
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1370.259
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1520.230
X-RAY DIFFRACTIONr_mcbond_it0.8031.51817
X-RAY DIFFRACTIONr_mcangle_it1.29822860
X-RAY DIFFRACTIONr_scbond_it1.98231192
X-RAY DIFFRACTIONr_scangle_it3.024.51042
LS refinement shellResolution: 1.6→1.641 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.317 208 -
Rwork0.291 3566 -
obs-3774 98.44 %

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