+Open data
-Basic information
Entry | Database: PDB / ID: 9be2 | ||||||
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Title | Structure of the E. coli nucleic associated protein, YejK | ||||||
Components | Nucleoid-associated protein YejK | ||||||
Keywords | DNA BINDING PROTEIN / NAP / nucleoid associated protein / YejK / NdpA / DNA binding clamp / non-sequence specific | ||||||
Function / homology | Nucleoid-associated protein NdpA / 37-kD nucleoid-associated bacterial protein / nucleoid / cytoplasm / Nucleoid-associated protein YejK Function and homology information | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 3.56 Å | ||||||
Authors | Schumacher, M.A. | ||||||
Funding support | United States, 1items
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Citation | Journal: Nucleic Acids Res. / Year: 2024 Title: Structure of the E. coli nucleoid-associated protein YejK reveals a novel DNA binding clamp. Authors: Schumacher, M.A. / Singh, R.R. / Salinas, R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 9be2.cif.gz | 146 KB | Display | PDBx/mmCIF format |
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PDB format | pdb9be2.ent.gz | 116.2 KB | Display | PDB format |
PDBx/mmJSON format | 9be2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 9be2_validation.pdf.gz | 421.2 KB | Display | wwPDB validaton report |
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Full document | 9be2_full_validation.pdf.gz | 428.1 KB | Display | |
Data in XML | 9be2_validation.xml.gz | 14.6 KB | Display | |
Data in CIF | 9be2_validation.cif.gz | 18.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/be/9be2 ftp://data.pdbj.org/pub/pdb/validation_reports/be/9be2 | HTTPS FTP |
-Related structure data
Similar structure data | Similarity search - Function & homologyF&H Search |
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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: 38145.660 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) Gene: yejK, ndpA, ACU57_09230, AM464_02260, BGM66_000319, BJI68_13225, CA593_16275, CG692_11175, CTR35_000614, DTL43_23020, E4K51_00810, E6D34_12665, EIZ93_06850, FOI11_002000, FOI11_18045, FV293_ ...Gene: yejK, ndpA, ACU57_09230, AM464_02260, BGM66_000319, BJI68_13225, CA593_16275, CG692_11175, CTR35_000614, DTL43_23020, E4K51_00810, E6D34_12665, EIZ93_06850, FOI11_002000, FOI11_18045, FV293_14640, FWK02_21355, G3V95_00395, GNW61_03255, GP965_18575, GP975_13725, GP979_05715, GQM21_07135, GRW05_06855, GRW56_16205, HMV95_16595, HMV95_25930, HVY77_09130, HX136_08035, J0541_002066, NCTC9073_01553, NCTC9706_04977, NCTC9962_03944, SAMEA3752557_00507 Production host: Escherichia (bacteria) / References: UniProt: A0A024L1K9 |
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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: 2.7 Å3/Da / Density % sol: 54.48 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop Details: 1.8 M sodium/potassium phosphate, 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: ALS / Beamline: 5.0.2 / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 12, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 3.56→42.56 Å / Num. obs: 4762 / % possible obs: 88.2 % / Redundancy: 7.4 % / CC1/2: 0.999 / Rpim(I) all: 0.031 / Rsym value: 0.081 / Net I/σ(I): 18.1 |
Reflection shell | Resolution: 3.56→4.05 Å / Mean I/σ(I) obs: 2.1 / Num. unique obs: 478 / CC1/2: 0.886 / Rpim(I) all: 0.0698 / Rsym value: 1.89 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 3.56→42.56 Å / SU ML: 0.6 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 35.43 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.56→42.56 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: -25.7341 Å / Origin y: 19.2245 Å / Origin z: 4.6917 Å
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Refinement TLS group | Selection details: all |