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- PDB-1pw8: Covalent Acyl Enzyme Complex Of The R61 DD-Peptidase with A Highl... -

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Basic information

Entry
Database: PDB / ID: 1pw8
TitleCovalent Acyl Enzyme Complex Of The R61 DD-Peptidase with A Highly Specific Cephalosporin
ComponentsD-alanyl-D-alanine carboxypeptidaseMuramoylpentapeptide carboxypeptidase
KeywordsHYDROLASE / BETA-LACTAM / ANTIBIOTICS / PENICILLIN BINDING PROTEIN / ENZYME / PEPTIDOGLYCAN
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-H2A / D-alanyl-D-alanine carboxypeptidase
Similarity search - Component
Biological speciesStreptomyces sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.3 Å
AuthorsSilvaggi, N.R. / Josephine, H.R. / Pratt, R.F. / Kelly, J.A.
Citation
Journal: J.Mol.Biol. / Year: 2005
Title: Crystal structures of complexes between the R61 DD-peptidase and peptidoglycan-mimetic beta-lactams: a non-covalent complex with a "perfect penicillin"
Authors: Silvaggi, N.R. / Josephine, H.R. / Kuzin, A.P. / Nagarajan, R. / Pratt, R.F. / Kelly, J.A.
#1: 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.
#2: Journal: Proc.Natl.Acad.Sci.USA / Year: 2001
Title: A 1.2-A Snapshot of the Final Step of Bacterial Cell Wall Biosynthesis
Authors: Lee, W. / Mcdonough, M.A. / Kotra, L. / Li, Z.H. / Silvaggi, N.R. / Takeda, Y. / Kelly, J.A. / Mobashery, S.
#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
DepositionJul 1, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 13, 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 1.3Jul 24, 2019Group: Data collection / Derived calculations / Refinement description
Category: software / struct_conn
Item: _software.classification / _software.name / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4Aug 16, 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_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 600ACYL FORM OF LIGAND H2A The ligand H2A in this structure is in its acylated form. The acylation ...ACYL FORM OF LIGAND H2A The ligand H2A in this structure is in its acylated form. The acylation reaction resulted in the removal of the covalent bond between atoms N5 and C8 of H2A 400, and the formation of the covalent bond between atom OG of SER 62 and atom C8 of H2A 400. MISSING LIGAND H2A ATOMS The following atoms are missing in the coordinate file for ligand CSC 400 in this structure: O1 C1 O2 C26

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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)38,0944
Polymers37,4231
Non-polymers6723
Water8,773487
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)50.800, 66.600, 98.700
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 37422.574 Da / Num. of mol.: 1 / Fragment: DD-PEPTIDASE / 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-H2A / (6R,7R)-3-[(ACETYLOXY)METHYL]-7-{[(6S)-6-(GLYCYLAMINO)-7-OXIDO-7-OXOHEPTANOYL]AMINO}-8-OXO-5-THIA-1-AZABICYCLO[4.2.0]OCTANE-2-CARBOXYLATE


Mass: 487.504 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H27N4O9S
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 487 / 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: 1.91 Å3/Da / Density % sol: 44.86 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.8
Details: 20% PEG 8000, 50mM Sodium Phosphate, pH 6.80, 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 / Wavelength: 1 Å
DetectorType: BRANDEIS - B4 / Detector: CCD / Date: Apr 12, 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: 1.3→50 Å / Num. all: 82877 / Num. obs: 82877 / % possible obs: 97.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 8.4 % / Rmerge(I) obs: 0.061 / Net I/σ(I): 23.3
Reflection shellResolution: 1.3→1.35 Å / Redundancy: 5.1 % / Rmerge(I) obs: 0.35 / Mean I/σ(I) obs: 3 / % possible all: 81.7

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Processing

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

3pte


Resolution: 1.3→10 Å / Num. parameters: 28501 / Num. restraintsaints: 34218 / Cross valid method: FREE R / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER
Details: ANISOTROPIC REFINEMENT REDUCED FREE R (NO CUTOFF) BY 0.031
RfactorNum. reflection% reflectionSelection details
Rfree0.1498 3897 5.3 %RANDOM
Rwork0.1076 ---
all0.1092 73703 --
obs0.1076 73703 89 %-
Refine analyzeLuzzati coordinate error obs: 0.06 Å / Num. disordered residues: 14 / Occupancy sum hydrogen: 243 / Occupancy sum non hydrogen: 3067.42
Refinement stepCycle: LAST / Resolution: 1.3→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2602 0 41 487 3130
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.034
X-RAY DIFFRACTIONs_angle_d0.038
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.0313
X-RAY DIFFRACTIONs_zero_chiral_vol0.077
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.083
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.04
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0.006
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.041
X-RAY DIFFRACTIONs_approx_iso_adps0.089

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