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Yorodumi- PDB-2qzb: Crystal structure of the uncharacterized protein yfeY from Escher... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2qzb | ||||||
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Title | Crystal structure of the uncharacterized protein yfeY from Escherichia coli | ||||||
Components | Uncharacterized protein yfeY | ||||||
Keywords | STRUCTURAL GENOMICS / UNKNOWN FUNCTION / PSI-2 / Protein Structure Initiative / New York SGX Research Center for Structural Genomics / NYSGXRC | ||||||
Function / homology | protein yfey like fold / protein yfey like domain / Protein of unknown function DUF1131 / YfeY-like superfamily / Protein of unknown function (DUF1131) / Sandwich / Mainly Beta / Uncharacterized protein YfeY Function and homology information | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.1 Å | ||||||
Authors | Bonanno, J.B. / Gilmore, M. / Bain, K.T. / Wu, B. / Romero, R. / Smith, D. / Wasserman, S. / Sauder, J.M. / Burley, S.K. / Almo, S.C. / New York SGX Research Center for Structural Genomics (NYSGXRC) | ||||||
Citation | Journal: To be Published Title: Crystal structure of the uncharacterized protein yfeY from Escherichia coli. Authors: Bonanno, J.B. / Gilmore, M. / Bain, K.T. / Wu, B. / Romero, R. / Smith, D. / Wasserman, S. / Sauder, J.M. / Burley, S.K. / Almo, S.C. | ||||||
History |
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Remark 300 | BIOMOLECULE: 1, 2 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND PROGRAM GENERATED ASSEMBLY ... BIOMOLECULE: 1, 2 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND PROGRAM GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN THIS ENTRY. AUTHORS STATE THAT THE MONOMERIC ASSEMBLY SHOWN IN REMARK 350 IS PROBABLE. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2qzb.cif.gz | 66.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2qzb.ent.gz | 52.5 KB | Display | PDB format |
PDBx/mmJSON format | 2qzb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2qzb_validation.pdf.gz | 434.8 KB | Display | wwPDB validaton report |
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Full document | 2qzb_full_validation.pdf.gz | 438.4 KB | Display | |
Data in XML | 2qzb_validation.xml.gz | 13.5 KB | Display | |
Data in CIF | 2qzb_validation.cif.gz | 18.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qz/2qzb ftp://data.pdbj.org/pub/pdb/validation_reports/qz/2qzb | 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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2 |
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Unit cell |
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Details | probable monomer |
-Components
#1: Protein | Mass: 18142.109 Da / Num. of mol.: 2 / Fragment: Residues 28-191 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: yfeY, b2432, JW2425 / Plasmid: Modified pET26 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P76537 #2: Water | ChemComp-HOH / | |
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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: 2.05 Å3/Da / Density % sol: 39.9 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion / pH: 8.5 Details: 100mM Tris-HCl pH 8.5, 2M Ammonium sulfate, VAPOR DIFFUSION, temperature 294K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.97958 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 28, 2007 |
Radiation | Monochromator: Silicon / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97958 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→37.45 Å / Num. all: 18942 / Num. obs: 18942 / % possible obs: 98.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 8 % / Biso Wilson estimate: 28.9 Å2 / Rmerge(I) obs: 0.09 / Rsym value: 0.09 / Net I/σ(I): 20.1 |
Reflection shell | Resolution: 2.1→2.21 Å / Redundancy: 6.4 % / Rmerge(I) obs: 0.238 / Mean I/σ(I) obs: 5.8 / Num. unique all: 2650 / Rsym value: 0.238 / % possible all: 96.6 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.1→20 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.883 / SU B: 5.394 / SU ML: 0.149 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.245 / ESU R Free: 0.23 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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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: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 32.552 Å2
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Refinement step | Cycle: LAST / Resolution: 2.1→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.1→2.154 Å / Total num. of bins used: 20
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