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Yorodumi- PDB-7uxg: Crystal structure of putative serine protease YdgD from Escherich... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7uxg | ||||||
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Title | Crystal structure of putative serine protease YdgD from Escherichia coli | ||||||
Components | Serine protease | ||||||
Keywords | HYDROLASE / putative peptidase / structural genomics / CSGID / Center for Structural Genomics of Infectious Diseases / NIAID / national institute of allergy and infectious diseases | ||||||
Function / homology | Function and homology information Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases / serine-type endopeptidase activity Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.24 Å | ||||||
Authors | Stogios, P.J. / Michalska, K. / Skarina, T. / Di Leo, R. / Savchenko, A. / Joachimiak, A. / Satchell, K.J.F. / Center for Structural Genomics of Infectious Diseases (CSGID) | ||||||
Funding support | United States, 1items
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Citation | Journal: To Be Published Title: Crystal structure of putative serine protease YdgD from Escherichia coli Authors: Stogios, P.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7uxg.cif.gz | 122 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7uxg.ent.gz | 85.2 KB | Display | PDB format |
PDBx/mmJSON format | 7uxg.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7uxg_validation.pdf.gz | 430.7 KB | Display | wwPDB validaton report |
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Full document | 7uxg_full_validation.pdf.gz | 438.2 KB | Display | |
Data in XML | 7uxg_validation.xml.gz | 11 KB | Display | |
Data in CIF | 7uxg_validation.cif.gz | 13.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ux/7uxg ftp://data.pdbj.org/pub/pdb/validation_reports/ux/7uxg | HTTPS FTP |
-Related structure data
Similar structure data | Similarity search - Function & homologyF&H Search |
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Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 29310.049 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) Gene: ydgD, ydgD_2, ACU57_22575, AWP93_25095, BANRA_00056, BJI68_03860, BJJ90_13150, BO068_000205, BON73_10185, BON74_16740, BON75_12740, BON77_15735, BON80_06260, BON89_22320, BON93_05710, BON98_ ...Gene: ydgD, ydgD_2, ACU57_22575, AWP93_25095, BANRA_00056, BJI68_03860, BJJ90_13150, BO068_000205, BON73_10185, BON74_16740, BON75_12740, BON77_15735, BON80_06260, BON89_22320, BON93_05710, BON98_16280, BvCmsHHP019_03974, C5N07_00380, CA593_20015, CG692_07775, CG831_003591, D0X26_02230, D3Y67_19900, DAH17_21610, DAH37_02090, DAH50_20815, DTL43_20775, E2119_03170, E2122_01640, E2131_13845, E2135_13145, E4K51_03735, E5P22_00880, E5P23_12110, E5P26_08885, E5P27_01355, E5P28_03650, E5P29_01740, E5P31_00130, E5P32_21155, E5P35_03725, E5P36_13145, E5P40_08615, E5P51_00995, E5S36_00460, E5S51_05780, E5S57_04080, EC1094V2_2155, EC3234A_33c00980, EI021_03345, EIZ93_12015, EL79_2119, EL80_2146, ELT20_01625, ELT41_03415, ELX85_00120, EYV17_14080, EYV18_16275, F2N31_02590, F9V24_02495, FQF29_12205, FTV90_17140, FV293_22055, G4A38_00120, GIB53_01320, GKF89_18985, GKG12_05835, GP979_01705, GQE64_03555, GRW05_00070, HMV95_01680, HNC36_07925, HX136_13140, IH768_09235, IH772_23575, J0541_000620, JNP96_14205, NCTC11126_06494, NCTC13216_04284, NCTC8008_01932, NCTC8500_02732, NCTC9037_02649, NCTC9045_02872, NCTC9706_03853, SAMEA3472044_02664, SAMEA3472067_01513, SAMEA3752557_01274, SAMEA3753106_04780, WP2S18E08_23190 Plasmid: pMCSG53 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): -Magic References: UniProt: W8T1B8, Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.06 Å3/Da / Density % sol: 40.31 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 25% PEG 3350, 0.2 M NaCl, 0.1 M Hepes pH 7.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.978 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 10, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.978 Å / Relative weight: 1 |
Reflection | Resolution: 2.24→50 Å / Num. obs: 11646 / % possible obs: 100 % / Redundancy: 19.7 % / Biso Wilson estimate: 78.3 Å2 / Rmerge(I) obs: 0.048 / Rpim(I) all: 0.011 / Net I/σ(I): 1.78 |
Reflection shell | Resolution: 2.25→2.29 Å / Redundancy: 16.8 % / Rmerge(I) obs: 1.585 / Mean I/σ(I) obs: 1.52 / Num. unique obs: 584 / CC1/2: 0.755 / Rpim(I) all: 0.392 / % possible all: 99.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: Alphafold2 Resolution: 2.24→42.5 Å / SU ML: 0.4641 / Cross valid method: FREE R-VALUE / σ(F): 0.25 / Phase error: 50.2333 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 115.65 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.24→42.5 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group | Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A
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