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- PDB-1sde: Toward Better Antibiotics: Crystal Structure Of D-Ala-D-Ala Pepti... -

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Basic information

Entry
Database: PDB / ID: 1sde
TitleToward Better Antibiotics: Crystal Structure Of D-Ala-D-Ala Peptidase inhibited by a novel bicyclic phosphate inhibitor
ComponentsD-alanyl-D-alanine carboxypeptidase
KeywordsHYDROLASE / CYCLIC PHOSPHATE / PEPTIDOGLYCAN / PENICILLIN BINDING PROTEIN / ANTIBIOTIC
Function / homology
Function and homology information


serine-type D-Ala-D-Ala carboxypeptidase / serine-type D-Ala-D-Ala carboxypeptidase activity / peptidoglycan biosynthetic process / cell wall organization / regulation of cell shape / proteolysis / extracellular region
Similarity search - Function
: / Beta-lactamase-related / Beta-lactamase / Beta-lactamase / DD-peptidase/beta-lactamase superfamily / Beta-lactamase/transpeptidase-like / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
2-[(DIOXIDOPHOSPHINO)OXY]BENZOATE / D-alanyl-D-alanine carboxypeptidase
Similarity search - Component
Biological speciesStreptomyces sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.15 Å
AuthorsSilvaggi, N.R. / Kaur, K. / Adediran, S.A. / Pratt, R.F. / Kelly, J.A.
Citation
Journal: Biochemistry / Year: 2004
Title: Toward better antibiotics: crystallographic studies of a novel class of DD-peptidase/beta-lactamase inhibitors
Authors: Silvaggi, N.R. / Kaur, K. / Adediran, S.A. / Pratt, R.F. / Kelly, J.A.
#1: Journal: Biochemistry / Year: 2003
Title: Structure of Phosphonate-Inhibited D-Ala-D-Ala Peptidase Reveals an Analogue of a Tetrahedral Transition State.
Authors: Silvaggi, N.R. / Anderson, J.W. / Brinsmade, S.R. / Pratt, R.F. / Kelly, J.A.
#2: Journal: J.Mol.Biol. / Year: 2002
Title: STRUCTURES OF TWO KINETIC INTERMEDIATES REVEAL SPECIES SPECIFICITY OF PENICILLIN-BINDING PROTEINS
Authors: McDonough, M.A. / Anderson, J.W. / Silvaggi, N.R. / Pratt, R.F. / Knox, J.R. / Kelly, J.A.
#3: Journal: J.Mol.Biol. / Year: 1995
Title: THE REFINED CRYSTALLOGRAPHIC STRUCTURE OF A DD-PEPTIDASE PENICILLIN-TARGET ENZYME AT 1.6A RESOLUTION
Authors: Kelly, J.A. / Kuzin, A.P.
History
DepositionFeb 13, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 12, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Aug 23, 2023Group: Data collection / Database references ...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 / 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
Revision 1.4Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)37,5133
Polymers37,2201
Non-polymers2922
Water10,233568
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)50.800, 66.700, 100.100
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsMonomer is biologically active unit

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Components

#1: Protein D-alanyl-D-alanine carboxypeptidase / DD-peptidase / DD-carboxypeptidase


Mass: 37220.371 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Streptomyces sp. (bacteria) / Strain: R61
References: UniProt: P15555, serine-type D-Ala-D-Ala carboxypeptidase
#2: Chemical ChemComp-2PB / 2-[(DIOXIDOPHOSPHINO)OXY]BENZOATE


Mass: 200.085 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H5O5P
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 18.015 Da / Num. of mol.: 568 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.28 Å3/Da / Density % sol: 46.01 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.8
Details: 20% PEG 8000, 50mM sodium phosphate, pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X12B / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 14, 2003 / Details: MIRRORS
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.15→50 Å / Num. all: 122116 / Num. obs: 119308 / % possible obs: 97.7 % / Observed criterion σ(I): 2 / Redundancy: 6.5 % / Rsym value: 0.056 / Net I/σ(I): 28.8
Reflection shellResolution: 1.15→1.19 Å / Redundancy: 4.3 % / Mean I/σ(I) obs: 4.3 / Num. unique all: 9967 / Rsym value: 0.245 / % possible all: 82.9

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Processing

Software
NameClassification
SHELXmodel building
SHELXL-97refinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 3PTE

3pte


Resolution: 1.15→10 Å / Num. parameters: 28915 / Num. restraintsaints: 0 / Cross valid method: FREE R / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER
Details: ANISOTROPIC REFINEMENT REDUCED FREE R (NO CUTOFF) BY 2.9%
RfactorNum. reflection% reflectionSelection details
Rfree0.1399 5813 5 %RANDOM
Rwork0.1013 ---
all0.1193 122116 --
obs0.1072 122116 94.3 %-
Displacement parametersBiso mean: 9.1 Å2
Refine analyzeNum. disordered residues: 25 / Occupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 3069.67
Refinement stepCycle: LAST / Resolution: 1.15→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2602 0 19 568 3189
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.014
X-RAY DIFFRACTIONs_angle_d0.03
X-RAY DIFFRACTIONs_from_restr_planes0.0312
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.096

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