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- PDB-1scw: TOWARD BETTER ANTIBIOTICS: CRYSTAL STRUCTURE OF R61 DD-PEPTIDASE ... -

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Basic information

Entry
Database: PDB / ID: 1scw
TitleTOWARD BETTER ANTIBIOTICS: CRYSTAL STRUCTURE OF R61 DD-PEPTIDASE INHIBITED BY A NOVEL MONOCYCLIC PHOSPHATE INHIBITOR
ComponentsD-alanyl-D-alanine carboxypeptidase
KeywordsHYDROLASE / CYCLIC PHOSPHATE / ANTIBIOTIC / PEPTIDOGLYCAN / PENICILLIN BINDING PROTEIN
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
Chem-CP5 / D-alanyl-D-alanine carboxypeptidase
Similarity search - Component
Biological speciesStreptomyces sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.13 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: THE CRYSTAL 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 1.6 A RESOLUTION
Authors: Kelly, J.A. / Kuzin, A.P.
History
DepositionFeb 12, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 22, 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 1.4Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)38,2008
Polymers37,4231
Non-polymers7787
Water9,188510
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)50.900, 66.700, 100.800
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsMonomer is biologically active form.

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Components

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


Mass: 37422.574 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-CP5 / (2Z)-3-{[OXIDO(OXO)PHOSPHINO]OXY}-2-PHENYLACRYLATE


Mass: 225.115 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H6O5P
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 510 / 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: 1.97 Å3/Da / Density % sol: 37.6 %
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: X12C / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 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: 1.13→50 Å / Num. all: 128693 / Num. obs: 120188 / % possible obs: 94.1 % / Observed criterion σ(I): 2 / Redundancy: 12.6 % / Rsym value: 0.062 / Net I/σ(I): 29.9
Reflection shellResolution: 1.13→1.17 Å / Redundancy: 6.5 % / Mean I/σ(I) obs: 15.6 / Num. unique all: 8991 / Rsym value: 0.091 / % possible all: 70.8

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Processing

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

3pte


Resolution: 1.13→10 Å / Num. parameters: 29594 / Num. restraintsaints: 37027 / Cross valid method: FREE R / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER
Details: ANISOTROPIC REFINEMENT REDUCED FREE R (NO CUTOFF) BY 1.2%.
RfactorNum. reflection% reflectionSelection details
Rfree0.1435 2737 2.3 %RANDOM
Rwork0.1023 ---
all0.1047 120188 --
obs0.104 120188 94.1 %-
Displacement parametersBiso mean: 8.9 Å2
Refine analyzeNum. disordered residues: 29 / Occupancy sum hydrogen: 326 / Occupancy sum non hydrogen: 3126.71
Refinement stepCycle: LAST / Resolution: 1.13→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2601 0 51 510 3162
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.024
X-RAY DIFFRACTIONs_angle_d0.033
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.032
X-RAY DIFFRACTIONs_zero_chiral_vol0.088
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.096
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.036
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0.006
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.033
X-RAY DIFFRACTIONs_approx_iso_adps0.1

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