+Open data
-Basic information
Entry | Database: PDB / ID: 2qni | ||||||
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Title | Crystal structure of uncharacterized protein Atu0299 | ||||||
Components | Uncharacterized protein Atu0299 | ||||||
Keywords | STRUCTURAL GENOMICS / UNKNOWN FUNCTION / MCSG / Atu0299 / In situ proteolysis / PSI-2 / Protein Structure Initiative / Midwest Center for Structural Genomics / Uncharacterized protein | ||||||
Function / homology | Phosphoglycerate mutase-like / Histidine phosphatase superfamily, clade-1 / Histidine phosphatase superfamily (branch 1) / Histidine phosphatase superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta / Uncharacterized protein / : Function and homology information | ||||||
Biological species | Agrobacterium tumefaciens str. (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.8 Å | ||||||
Authors | Dong, A. / Xu, X. / Gu, J. / Zheng, H. / Edwards, A.M. / Joachimiak, A. / Savchenko, A. / Midwest Center for Structural Genomics (MCSG) | ||||||
Citation | Journal: To be Published Title: Crystal structure of uncharacterized protein Atu0299. Authors: Dong, A. / Xu, X. / Gu, J. / Zheng, H. / Edwards, A.M. / Joachimiak, A. / Savchenko, A. | ||||||
History |
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Remark 300 | BIOMOLECULE: 1 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND PROGRAM GENERATED ASSEMBLY INFORMATION ... BIOMOLECULE: 1 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND PROGRAM GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON BURIED SURFACE AREA. AUTHORS STATE THAT THE BIOLOGICAL UNIT INFORMATION OF THIS PROTEIN IS NOT AVAILABLE. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2qni.cif.gz | 51.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2qni.ent.gz | 39.7 KB | Display | PDB format |
PDBx/mmJSON format | 2qni.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qn/2qni ftp://data.pdbj.org/pub/pdb/validation_reports/qn/2qni | HTTPS FTP |
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-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: 24388.555 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 / Gene: AGR_C_517, Atu0299 / Plasmid: pET derivative / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) derivative / References: UniProt: Q8UIJ6, UniProt: A9CKF0*PLUS |
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#2: 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: 3.33 Å3/Da / Density % sol: 63.03 % Description: Due to a number of circumstances, initial data processing was only accomplished in space group C2. Scaling statistics is provided for that space group. Using the program XPREP, the ...Description: Due to a number of circumstances, initial data processing was only accomplished in space group C2. Scaling statistics is provided for that space group. Using the program XPREP, the higher symmetry (H32) was detected and used in refinement. The structure factor file contains both data sets: for H32 and for C2 space group assignments |
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Crystal grow | Temperature: 297 K / Method: vapor diffusion, sitting drop / pH: 4.6 Details: 0.1M Na(OAC) pH 4.6, 3.5M Sodium formate. THE CRYSTAL WAS OBTAINED BY IN SITU PROTEOLYSIS, PROTEIN SAMPLE WAS MIXED WITH 1:100 WEIGHT TO WEIGHT RATIO WITH CHYMOTRYPSIN IMMEDIATELY PRIOR TO ...Details: 0.1M Na(OAC) pH 4.6, 3.5M Sodium formate. THE CRYSTAL WAS OBTAINED BY IN SITU PROTEOLYSIS, PROTEIN SAMPLE WAS MIXED WITH 1:100 WEIGHT TO WEIGHT RATIO WITH CHYMOTRYPSIN IMMEDIATELY PRIOR TO SETTING UP CRYSTALLIZATION, VAPOR DIFFUSION, SITTING DROP, temperature 297K Temp details: THE CRYSTAL WAS OBTAINED BY IN SITU PROTEOLYSIS, PROTEIN SAMPLE WAS MIXED WITH 1:100 WEIGHT TO WEIGHT RATIO WITH CHYMOTRYPSIN IMMEDIATELY PRIOR TO SETTING UP CRYSTALLIZATION |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 0.976 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: May 5, 2007 |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.976 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→50 Å / Num. all: 88206 / Num. obs: 88206 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.5 % / Biso Wilson estimate: 28.4 Å2 / Rmerge(I) obs: 0.061 / Rsym value: 0.061 / Net I/σ(I): 10.9 |
Reflection shell | Resolution: 1.8→1.86 Å / Redundancy: 6.1 % / Rmerge(I) obs: 0.749 / Mean I/σ(I) obs: 1.92 / Num. unique all: 8762 / Rsym value: 0.749 / % possible all: 99.3 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.8→50 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.945 / SU B: 2.034 / SU ML: 0.065 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.099 / ESU R Free: 0.096 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. ARP/wARP 6.1.1 and COOT 0.1 programs were also used in refinement
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 28.7 Å2
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Refinement step | Cycle: LAST / Resolution: 1.8→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.8→1.85 Å / Total num. of bins used: 20
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