+Open data
-Basic information
Entry | Database: PDB / ID: 1k4n | ||||||
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Title | Structural Genomics, Protein EC4020 | ||||||
Components | Protein EC4020 | ||||||
Keywords | STRUCTURAL GENOMICS / UNKNOWN FUNCTION / A new fold of protein / PSI / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG | ||||||
Function / homology | Protein of unknown function DUF991, YecM-like / YecM protein / 2,3-Dihydroxybiphenyl 1,2-Dioxygenase, domain 1 / 2,3-Dihydroxybiphenyl 1,2-Dioxygenase; domain 1 / Glyoxalase/Bleomycin resistance protein/Dihydroxybiphenyl dioxygenase / Roll / cytosol / Alpha Beta / Protein YecM Function and homology information | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.6 Å | ||||||
Authors | Zhang, R.G. / Joachimiak, A. / Edwards, A. / Savchenko, A. / Skarina, T. / Midwest Center for Structural Genomics (MCSG) | ||||||
Citation | Journal: Proteins / Year: 2003 Title: Conserved protein YecM from Escherichia coli shows structural homology to metal-binding isomerases and oxygenases. Authors: Zhang, R.G. / Duke, N. / Laskowski, R. / Evdokimova, E. / Skarina, T. / Edwards, A. / Joachimiak, A. / Savchenko, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1k4n.cif.gz | 51 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1k4n.ent.gz | 39.1 KB | Display | PDB format |
PDBx/mmJSON format | 1k4n.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/k4/1k4n ftp://data.pdbj.org/pub/pdb/validation_reports/k4/1k4n | 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: 21811.229 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli) / References: UniProt: P52007 |
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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: 1.96 Å3/Da / Density % sol: 37.18 % | ||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / Details: VAPOR DIFFUSION, HANGING DROP, temperature 298K | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 7.5 | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9795, 0.9798, 0.94656 | ||||||||||||
Detector | Type: SBC-2 / Detector: CCD / Date: Aug 8, 2001 / Details: mirrors | ||||||||||||
Radiation | Monochromator: Si 111 CHANNEL / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||
Radiation wavelength |
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Reflection | Resolution: 1.6→50 Å / Num. all: 24450 / Num. obs: 24275 / % possible obs: 99.3 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 4 / Redundancy: 7.9 % / Biso Wilson estimate: 13.5 Å2 / Rmerge(I) obs: 0.049 / Net I/σ(I): 25.1 | ||||||||||||
Reflection shell | Resolution: 1.58→1.66 Å / Redundancy: 5 % / Rmerge(I) obs: 0.258 / Mean I/σ(I) obs: 5.3 / Num. unique all: 3402 / % possible all: 99.4 | ||||||||||||
Reflection | *PLUS Redundancy: 6.9 % |
-Processing
Software |
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Refinement | Resolution: 1.6→38.86 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 405396.38 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 45.6398 Å2 / ksol: 0.372806 e/Å3 | ||||||||||||||||||||
Displacement parameters | Biso mean: 18.5 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.6→38.86 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.6→1.7 Å / Rfactor Rfree error: 0.012 / Total num. of bins used: 6
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Xplor file |
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Refinement | *PLUS Lowest resolution: 50 Å / Num. reflection all: 24450 / Num. reflection obs: 23643 | ||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||
Refine LS restraints | *PLUS
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