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- PDB-1hvb: CRYSTAL STRUCTURE OF STREPTOMYCES R61 DD-PEPTIDASE COMPLEXED WITH... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1hvb | ||||||
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Title | CRYSTAL STRUCTURE OF STREPTOMYCES R61 DD-PEPTIDASE COMPLEXED WITH A NOVEL CEPHALOSPORIN ANALOG OF CELL WALL PEPTIDOGLYCAN | ||||||
![]() | D-ALANYL-D-ALANINE CARBOXYPEPTIDASE | ||||||
![]() | HYDROLASE / Protein-cephalosporin complex | ||||||
Function / homology | ![]() 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 | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | McDonough, M.A. / Lee, W. / Silvaggi, N.R. / Mobashery, S. / Kelly, J.A. | ||||||
![]() | ![]() 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. #1: ![]() Title: Binding of Cephalothin and Cefotaxime to D-Ala-D-Ala-Peptidase Reveals A Functional Basis of a Natural Mutation in a Low-Affinity Penicillin-Binding Protein and in Extended-Spectrum Beta-Lactamases Authors: Kuzin, A.P. / Liu, H. / Kelly, J.A. / Knox, J.R. #2: ![]() Title: The Refined Crystallographic Structure of a DD-Peptidase Penicillin-target Enzyme at 1.6 Angstrom Resolution Authors: Kelly, J.A. / Kuzin, A.P. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 179.9 KB | Display | ![]() |
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PDB format | ![]() | 141.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 468 KB | Display | ![]() |
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Full document | ![]() | 474.8 KB | Display | |
Data in XML | ![]() | 9.8 KB | Display | |
Data in CIF | ![]() | 17.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3pteS S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 |
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Unit cell |
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Components
#1: Protein | Mass: 37422.574 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() References: UniProt: P15555, serine-type D-Ala-D-Ala carboxypeptidase |
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#2: Chemical | ChemComp-CEH / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.94 Å3/Da / Density % sol: 36.6 % | |||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.8 Details: PEG 8000, sodium phosphate, pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 298K | |||||||||||||||
Crystal grow | *PLUS Method: unknown / Details: Kuzin, A.P., (1995) Biochemistry, 34, 9532. | |||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: BRANDEIS - B4 / Detector: CCD / Date: Jan 29, 2000 / Details: Monochromator, Mirror |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 1.17→20 Å / Num. all: 2330719 / Num. obs: 111370 / % possible obs: 95.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5 % / Biso Wilson estimate: 18.6 Å2 / Rmerge(I) obs: 0.04 / Net I/σ(I): 25 |
Reflection shell | Resolution: 1.17→1.21 Å / Rmerge(I) obs: 0.162 / Mean I/σ(I) obs: 4.6 / Num. unique all: 8392 / % possible all: 72.9 |
Reflection | *PLUS Num. measured all: 2330719 / Rmerge(I) obs: 0.04 |
Reflection shell | *PLUS % possible obs: 73 % |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 3PTE Resolution: 1.17→10 Å / Num. parameters: 29978 / Num. restraintsaints: 36742 / Isotropic thermal model: ISOTROPIC / Cross valid method: free r / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER Details: THE ESTIMATED STANDARD DEVIATION OF ATOMIC COORDINATES FOR ALL ATOMS IS 0.032 ANGSTROMS DETERMINED BY INVERSION OF THE LEAST-SQUARES MATRIX. ANISOTROPIC REFINEMENT REDUCED FREE R (NO CUTOFF) ...Details: THE ESTIMATED STANDARD DEVIATION OF ATOMIC COORDINATES FOR ALL ATOMS IS 0.032 ANGSTROMS DETERMINED BY INVERSION OF THE LEAST-SQUARES MATRIX. ANISOTROPIC REFINEMENT REDUCED FREE R (NO CUTOFF) BY 3.5%. WATER MOLECULES DESIGNATED AS B CONFORMATION ARE PRESENT IN UN-LIGAND BOUND MOLECULES IN THE CRYSTAL.
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Solvent computation | Solvent model: MOEWS & KRETSINGER, J.MOL.BIOL.91(1973)201-228 | |||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 16.1 Å2 | |||||||||||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.146 Å / Luzzati d res low obs: 20 Å / Num. disordered residues: 35 / Occupancy sum hydrogen: 268.92 / Occupancy sum non hydrogen: 3181.8 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.17→10 Å
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Refine LS restraints |
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Software | *PLUS Name: SHELXL-97 / Classification: refinement | |||||||||||||||||||||||||||||||||
Refinement | *PLUS σ(F): 0 / % reflection Rfree: 5 % | |||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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