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Yorodumi- PDB-3k5x: Crystal structure of dipeptidase from Streptomics coelicolor comp... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3k5x | ||||||
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Title | Crystal structure of dipeptidase from Streptomics coelicolor complexed with phosphinate pseudodipeptide L-Ala-D-Asp at 1.4A resolution. | ||||||
Components | Dipeptidase | ||||||
Keywords | HYDROLASE / dipeptidase from Streptomics coelicolor / the closest bacterial homolog to human renal dipeptidase / phosphinate pseudodipeptide / L-Ala-D-Asp | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Streptomyces coelicolor (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å | ||||||
Model details | Putative dipeptidase | ||||||
Authors | Fedorov, A.A. / Fedorov, E.V. / Cummings, J. / Raushel, F.M. / Almo, S.C. | ||||||
Citation | Journal: Biochemistry / Year: 2010 Title: Structure, mechanism, and substrate profile for Sco3058: the closest bacterial homologue to human renal dipeptidase . Authors: Cummings, J.A. / Nguyen, T.T. / Fedorov, A.A. / Kolb, P. / Xu, C. / Fedorov, E.V. / Shoichet, B.K. / Barondeau, D.P. / Almo, S.C. / Raushel, F.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3k5x.cif.gz | 97.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3k5x.ent.gz | 72.4 KB | Display | PDB format |
PDBx/mmJSON format | 3k5x.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/k5/3k5x ftp://data.pdbj.org/pub/pdb/validation_reports/k5/3k5x | HTTPS FTP |
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-Related structure data
Related structure data | 3id7SC 3itcC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 43306.137 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptomyces coelicolor (bacteria) / Gene: SCO3058, SCBAC19G2.13c / Production host: Escherichia coli (E. coli) / References: UniProt: Q93J45 | ||
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#2: Chemical | ChemComp-P8D / | ||
#3: Chemical | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.26 Å3/Da / Density % sol: 62.28 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 22% polyacrylic acid, 0.1M hepes, 0.02M magnesium chloride, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.97915 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Oct 3, 2009 |
Radiation | Monochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97915 Å / Relative weight: 1 |
Reflection | Resolution: 1.4→25 Å / Num. all: 106229 / Num. obs: 106229 / % possible obs: 95.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 16.4 Å2 / Rmerge(I) obs: 0.072 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3ID7 Resolution: 1.4→24.88 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 1767382.58 / 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: 58.91 Å2 / ksol: 0.366725 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 16.6 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.4→24.88 Å
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Refine LS restraints |
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Refine LS restraints NCS | NCS model details: NONE | ||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.4→1.45 Å / Rfactor Rfree error: 0.019 / Total num. of bins used: 10
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Xplor file |
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