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- PDB-1ikg: MICHAELIS COMPLEX OF STREPTOMYCES R61 DD-PEPTIDASE WITH A SPECIFI... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1ikg | ||||||
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Title | MICHAELIS COMPLEX OF STREPTOMYCES R61 DD-PEPTIDASE WITH A SPECIFIC PEPTIDOGLYCAN SUBSTRATE FRAGMENT | ||||||
![]() | D-ALANYL-D-ALANINE CARBOXYPEPTIDASE | ||||||
![]() | HYDROLASE / MICHAELIS COMPLEX / PEPTIDOGLYCAN / PENICILLIN BINDING PROTEIN | ||||||
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. / Anderson, J.W. / Silvaggi, N.R. / Pratt, R.F. / Knox, J.R. / Kelly, J.A. | ||||||
![]() | ![]() 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. #1: ![]() 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. #2: ![]() 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. #3: ![]() 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 |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 88.1 KB | Display | ![]() |
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PDB format | ![]() | 64.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 419.1 KB | Display | ![]() |
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Full document | ![]() | 420.6 KB | Display | |
Data in XML | ![]() | 8.3 KB | Display | |
Data in CIF | ![]() | 14.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1ikiC ![]() 3pteS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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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-REX / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.27 Å3/Da / Density % sol: 45.9 % | ||||||||||||||||||||||||
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Crystal grow | Method: vapor diffusion, hanging drop / pH: 6.8 Details: PEG 8000, SODIUM PHOSPHATE, pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 100K | ||||||||||||||||||||||||
Crystal grow | *PLUS | ||||||||||||||||||||||||
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: SIEMENS HI-STAR / Detector: AREA DETECTOR / Date: Nov 13, 1999 / Details: MIRRORS |
Radiation | Monochromator: Ni FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.542 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→28 Å / Num. all: 28134 / Num. obs: 26003 / % possible obs: 99 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 3.4 % / Biso Wilson estimate: 7.7 Å2 / Rsym value: 0.044 / Net I/σ(I): 22.5 |
Reflection shell | Resolution: 1.9→2.02 Å / Redundancy: 2.4 % / Num. unique all: 2978 / Rsym value: 0.086 / % possible all: 70 |
Reflection | *PLUS Lowest resolution: 28 Å / % possible obs: 93 % / Num. measured all: 130497 / Rmerge(I) obs: 0.044 |
Reflection shell | *PLUS Highest resolution: 1.9 Å / % possible obs: 70 % / Rmerge(I) obs: 0.086 / Mean I/σ(I) obs: 10 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 3PTE Resolution: 1.9→27.93 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 155199.09 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: ENGH & HUBER
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 67.12 Å2 / ksol: 0.373 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 9.9 Å2
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Refine analyze | Num. disordered residues: 3
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Refinement step | Cycle: LAST / Resolution: 1.9→27.93 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.9→2.02 Å / Rfactor Rfree error: 0.018 / Total num. of bins used: 6
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Xplor file |
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Refinement | *PLUS Lowest resolution: 28 Å / Rfactor all: 0.15 / Rfactor Rwork: 0.15 | ||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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