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- PDB-1hd8: Crystal structure of a deacylation-defective mutant of penicillin... -

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Basic information

Entry
Database: PDB / ID: 1hd8
TitleCrystal structure of a deacylation-defective mutant of penicillin-binding protein 5 at 2.3 A resolution
ComponentsPENICILLIN-BINDING PROTEIN 5
KeywordsHYDROLASE / PEPTIDOGLYCAN SYNTHESIS / PENICILLIN-BINDING PROTEIN / DD-CARBOXYPEPTIDASE
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 / cell division / 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
D-alanyl-D-alanine carboxypeptidase DacA / D-alanyl-D-alanine carboxypeptidase DacA
Similarity search - Component
Biological speciesESCHERICHIA COLI (E. coli)
MethodX-RAY DIFFRACTION / MIR / Resolution: 2.3 Å
AuthorsDavies, C. / White, S.W. / Nicholas, R.A.
Citation
Journal: J.Biol.Chem. / Year: 2001
Title: Crystal Structure of a Deacylation-Defective Mutant of Penicillin-Binding Protein 5 at 2.3-A Resolution
Authors: Davies, C. / White, S.W. / Nicholas, R.A.
#1: Journal: Rev.Infect.Dis. / Year: 1988
Title: Relations between Beta-Lactamases and Penicillin-Binding Proteins: Beta-Lactamase Activity of Penicillin-Binding Protein 5 from Escherichia Coli
Authors: Nicholas, R.A. / Strominger, J.L.
#2: Journal: FEBS Lett. / Year: 1984
Title: An Amino Acid Substitution that Blocks the Deacylation Step in the Enzyme Mechanism of Penicillin-Binding Protein 5 of Escherichia Coli
Authors: Broome-Smith, J. / Spratt, B.G.
History
DepositionNov 11, 2000Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 8, 2001Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 8, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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: PENICILLIN-BINDING PROTEIN 5


Theoretical massNumber of molelcules
Total (without water)39,8991
Polymers39,8991
Non-polymers00
Water2,612145
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)50.830, 50.830, 140.290
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number145
Space group name H-MP32

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Components

#1: Protein PENICILLIN-BINDING PROTEIN 5


Mass: 39899.152 Da / Num. of mol.: 1 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Cellular location: PERIPLASM / Gene: DACA / Plasmid: PBR322 / Gene (production host): DACA / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): MC1061
References: UniProt: P04287, UniProt: P0AEB2*PLUS, serine-type D-Ala-D-Ala carboxypeptidase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 145 / Source method: isolated from a natural source / Formula: H2O
Compound detailsCHAIN A ENGINEERED MUTATION GLY105ASP TO PRODUCE SPBP 5', THE LAST 17 AMINO ACIDS WERE REMOVED BY ...CHAIN A ENGINEERED MUTATION GLY105ASP TO PRODUCE SPBP 5', THE LAST 17 AMINO ACIDS WERE REMOVED BY DELETION OF THEIR RESPECTIVE CODONS, BUT 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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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.06 Å3/Da / Density % sol: 59.5 %
Crystal growpH: 7
Details: 20% POLYETHYLENE GLYCOL 4000, 50 MM TRIS PH 7.0, 0.2 % SODIUM AZIDE
Crystal grow
*PLUS
Temperature: 18 ℃ / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
120 %PEG40001reservoir
250 mMTris-HCl1reservoir
30.2 %1reservoirNaN3

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: ROTATING ANODE / Type: NONIUS FR391 / Wavelength: 1.5418
DetectorType: MACSCIENCE / Detector: IMAGE PLATE / Date: Dec 15, 1998 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.3→22.4 Å / Num. obs: 17239 / % possible obs: 94.8 % / Redundancy: 2.52 % / Biso Wilson estimate: 28.41 Å2 / Rsym value: 0.069 / Net I/σ(I): 13.2
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 1.9 % / Mean I/σ(I) obs: 3.3 / Rsym value: 0.294 / % possible all: 85.2
Reflection
*PLUS
Num. measured all: 43406 / Rmerge(I) obs: 0.069

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Processing

Software
NameClassification
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
SHARPphasing
RefinementMethod to determine structure: MIR / Resolution: 2.3→15 Å / SU B: 8.6 / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.372 / ESU R Free: 0.284 / Details: XPLOR USED IN EARLY STAGES OF REFINEMENT
RfactorNum. reflection% reflectionSelection details
Rfree0.283 1693 10 %RANDOM
Rwork0.199 ---
obs0.207 17184 95.4 %-
Displacement parametersBiso mean: 35.44 Å2
Refinement stepCycle: LAST / Resolution: 2.3→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2606 0 0 145 2751
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0130.02
X-RAY DIFFRACTIONp_angle_d0.0430.04
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0740.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it1.6422
X-RAY DIFFRACTIONp_mcangle_it2.5413
X-RAY DIFFRACTIONp_scbond_it1.8642
X-RAY DIFFRACTIONp_scangle_it2.923
X-RAY DIFFRACTIONp_plane_restr0.02440.03
X-RAY DIFFRACTIONp_chiral_restr0.1480.15
X-RAY DIFFRACTIONp_singtor_nbd0.1910.3
X-RAY DIFFRACTIONp_multtor_nbd0.2570.3
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd0.1870.3
X-RAY DIFFRACTIONp_planar_tor9.87
X-RAY DIFFRACTIONp_staggered_tor19.915
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor22.820
X-RAY DIFFRACTIONp_special_tor
Software
*PLUS
Name: REFMAC / Classification: refinement
Refinement
*PLUS
Num. reflection obs: 17208 / Rfactor all: 0.207 / Rfactor obs: 0.196 / Rfactor Rfree: 0.27
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.011
X-RAY DIFFRACTIONp_dihedral_angle_d
X-RAY DIFFRACTIONp_dihedral_angle_deg24.73
X-RAY DIFFRACTIONp_improper_angle_d
X-RAY DIFFRACTIONp_improper_angle_deg2.552

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