+Open data
-Basic information
Entry | Database: PDB / ID: 7by2 | ||||||
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Title | Toxin-antitoxin complex from Klebsiella pneumoniae | ||||||
Components |
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Keywords | HYDROLASE / protein complex | ||||||
Function / homology | Function and homology information RNA nuclease activity / toxin activity / sequence-specific DNA binding / Hydrolases; Acting on ester bonds / regulation of DNA-templated transcription / magnesium ion binding Similarity search - Function | ||||||
Biological species | Klebsiella pneumoniae (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.6 Å | ||||||
Authors | Kang, S.M. | ||||||
Funding support | 1items
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Citation | Journal: To Be Published Title: Toxin-antitoxin complex from Klebsiella pneumoniae Authors: Kang, S.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7by2.cif.gz | 41.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7by2.ent.gz | 30.7 KB | Display | PDB format |
PDBx/mmJSON format | 7by2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7by2_validation.pdf.gz | 433.7 KB | Display | wwPDB validaton report |
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Full document | 7by2_full_validation.pdf.gz | 436 KB | Display | |
Data in XML | 7by2_validation.xml.gz | 8.2 KB | Display | |
Data in CIF | 7by2_validation.cif.gz | 9.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/by/7by2 ftp://data.pdbj.org/pub/pdb/validation_reports/by/7by2 | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 9799.104 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Klebsiella pneumoniae (bacteria) Gene: yiiF, B4U21_30180, B4U25_36990, B4U61_14815, B6R99_17700, BANRA_02143, BANRA_02521, BANRA_02705, BL124_00012815, BN49_4676, C2U49_19540, C3F39_14645, C4Y50_020990, C7V41_25295, CK508_014375, ...Gene: yiiF, B4U21_30180, B4U25_36990, B4U61_14815, B6R99_17700, BANRA_02143, BANRA_02521, BANRA_02705, BL124_00012815, BN49_4676, C2U49_19540, C3F39_14645, C4Y50_020990, C7V41_25295, CK508_014375, DD581_07355, DD583_18720, DM059_31040, DM060_29565, DM062_35665, DM078_20205, EAO17_14145, EXT45_23360, F0330_15215, F1D54_19805, F3G17_14565, F3G25_25430, FAM29_17470, FAT93_13335, FCH06_017260, FXN60_10800, FXN67_21280, FZ928_20910, FZ929_16080, NCTC11679_05637, NCTC13443_00678, NCTC13635_03530, NCTC204_01866, NCTC8849_00074, NCTC9128_03825, NCTC9140_00751, NCTC9617_03579, NCTC9637_06504, SAMEA104567806_05449, SAMEA104567903_04890, SAMEA1712987_04768, SAMEA24002668_04178, SAMEA3531867_04820, SAMEA3649709_04060, SAMEA3673128_04237, SAMEA4364603_04577, SAMEA4873575_05060, SK89_02101 Production host: Escherichia coli (E. coli) / References: UniProt: W9BQC4 |
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#2: Protein | Mass: 14582.157 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Klebsiella pneumoniae (bacteria) Gene: vapC, B4U21_30185, B4U61_14820, B6R99_17695, BANRA_02522, BL124_00012810, BN49_4675, C1459_03020, C2U49_19545, C3F39_14640, C4Y50_020995, C7V41_25300, CK508_014380, DD581_07360, DM060_29570, ...Gene: vapC, B4U21_30185, B4U61_14820, B6R99_17695, BANRA_02522, BL124_00012810, BN49_4675, C1459_03020, C2U49_19545, C3F39_14640, C4Y50_020995, C7V41_25300, CK508_014380, DD581_07360, DM060_29570, DM078_20200, EAO17_14150, F1D54_19800, F3G25_25425, FAT93_13340, FCH06_017265, FXN60_10805, NCTC11679_05636, NCTC13443_00679, NCTC13465_05507, NCTC1936_00156, NCTC204_01865, NCTC8849_00075, NCTC9128_03826, SAMEA104567806_05448, SAMEA1712987_04767, SAMEA24002668_04177, SAMEA3531867_04819, SAMEA3649709_04059, SAMEA3673128_04238, SK89_02102 Production host: Escherichia coli (E. coli) References: UniProt: A0A0W8AM92, Hydrolases; Acting on ester bonds |
#3: Water | ChemComp-HOH / |
Has ligand of interest | N |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.68 Å3/Da / Density % sol: 54.1 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: Tris |
-Data collection
Diffraction | Mean temperature: 193 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.9794 Å |
Detector | Type: ADSC QUANTUM 270 / Detector: CCD / Date: Nov 3, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9794 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→50 Å / Num. obs: 8245 / % possible obs: 99.9 % / Redundancy: 13.4 % / Rpim(I) all: 0.054 / Net I/σ(I): 57.8 |
Reflection shell | Resolution: 2.6→2.64 Å / Num. unique obs: 397 / Rpim(I) all: 0.0632 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.6→50 Å / Cross valid method: FREE R-VALUE
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Displacement parameters | Biso mean: 75.43 Å2 | ||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.6→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.6→2.64 Å /
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