+Open data
-Basic information
Entry | Database: PDB / ID: 2hly | ||||||
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Title | The crystal structure of genomics APC5867 | ||||||
Components | Hypothetical protein Atu2299 | ||||||
Keywords | STRUCTURAL GENOMICS / UNKNOWN FUNCTION / ATC2257 / MCSG / PSI-2 / Protein Structure Initiative / Midwest Center for Structural Genomics | ||||||
Function / homology | Function and homology information Atu2299-like / Hypothetical protein Atu2299 / Protein of unknown function DUF2026 / Atu2299-like domain superfamily / Protein of unknown function (DUF2026) / Papain-like cysteine peptidase superfamily / Roll / Alpha Beta Similarity search - Domain/homology | ||||||
Biological species | Agrobacterium tumefaciens str. (bacteria) | ||||||
Method | X-RAY DIFFRACTION / Sulfur SAD / Resolution: 1.6 Å | ||||||
Authors | Dong, A. / Xu, X. / Zheng, H. / Kim, Y. / Edwards, A.M. / Joachimiak, A. / Savchenko, A. / Midwest Center for Structural Genomics (MCSG) | ||||||
Citation | Journal: TO BE PUBLISHED Title: The crystal structure of genomics APC5867 Authors: Dong, A. / Xu, X. / Zheng, H. / Kim, Y. / Edwards, A.M. / Joachimiak, A. / Savchenko, A. | ||||||
History |
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Remark 300 | BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 1 CHAIN(S) ...BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 1 CHAIN(S). AUTHOR STATES THAT THE BIOLOGICAL UNIT OF THIS PROTEIN IS UNKNOWN. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2hly.cif.gz | 58.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2hly.ent.gz | 42.4 KB | Display | PDB format |
PDBx/mmJSON format | 2hly.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2hly_validation.pdf.gz | 417.3 KB | Display | wwPDB validaton report |
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Full document | 2hly_full_validation.pdf.gz | 418.5 KB | Display | |
Data in XML | 2hly_validation.xml.gz | 12.4 KB | Display | |
Data in CIF | 2hly_validation.cif.gz | 18.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hl/2hly ftp://data.pdbj.org/pub/pdb/validation_reports/hl/2hly | HTTPS FTP |
-Related structure data
Similar structure data | |
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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: 22771.750 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Agrobacterium tumefaciens str. (bacteria) Species: Agrobacterium tumefaciens / Strain: C58 / Plasmid: p15Tv lic / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q8UD29, UniProt: A9CI22*PLUS |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 2 |
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-Sample preparation
Crystal | Density Matthews: 2 Å3/Da / Density % sol: 38.65 % |
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Crystal grow | Temperature: 297 K / Method: vapor diffusion / pH: 6 Details: 0.1M Bis-Tris pH 6.0, 1.5M Ammonium Sulphate, VAPOR DIFFUSION, temperature 297K |
-Data collection
Diffraction |
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Diffraction source |
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Detector |
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Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||
Radiation wavelength |
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Reflection | Resolution: 1.6→50 Å / Num. all: 23511 / Num. obs: 23511 / % possible obs: 94.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.8 % / Biso Wilson estimate: 18.1 Å2 / Rmerge(I) obs: 0.037 / Rsym value: 0.037 / Net I/σ(I): 30 | |||||||||||||||
Reflection shell | Resolution: 1.6→1.63 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.1 / Mean I/σ(I) obs: 9.4 / Num. unique all: 690 / Rsym value: 0.1 / % possible all: 57 |
-Processing
Software |
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Refinement | Method to determine structure: Sulfur SAD / Resolution: 1.6→42.84 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.94 / SU B: 1.461 / SU ML: 0.054 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.1 / ESU R Free: 0.101 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. BOTH REFMAC AND COOT ARE USED FOR REFINEMENT.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 17.875 Å2
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Refinement step | Cycle: LAST / Resolution: 1.6→42.84 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.6→1.642 Å / Total num. of bins used: 20
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