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Yorodumi- PDB-4xfm: Crystal structure of a domain of unknown function (DUF1537) from ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4xfm | ||||||
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Title | Crystal structure of a domain of unknown function (DUF1537) from Pectobacterium atrosepticum (ECA3761), Target EFI-511609, with bound D-threonate, domain swapped dimer | ||||||
Components | Uncharacterized protein | ||||||
Keywords | Structural Genomics / Unknown function / ENZYME FUNCTION INITIATIVE / EFI | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Pectobacterium atrosepticum (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 Å | ||||||
Authors | Vetting, M.W. / Al Obaidi, N.F. / Toro, R. / Morisco, L.L. / Benach, J. / Wasserman, S.R. / Attonito, J.D. / Scott Glenn, A. / Chamala, S. / Chowdhury, S. ...Vetting, M.W. / Al Obaidi, N.F. / Toro, R. / Morisco, L.L. / Benach, J. / Wasserman, S.R. / Attonito, J.D. / Scott Glenn, A. / Chamala, S. / Chowdhury, S. / Lafleur, J. / Love, J. / Seidel, R.D. / Whalen, K.L. / Gerlt, J.A. / Almo, S.C. / Enzyme Function Initiative (EFI) | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2016 Title: Assignment of function to a domain of unknown function: DUF1537 is a new kinase family in catabolic pathways for acid sugars. Authors: Zhang, X. / Carter, M.S. / Vetting, M.W. / San Francisco, B. / Zhao, S. / Al-Obaidi, N.F. / Solbiati, J.O. / Thiaville, J.J. / de Crecy-Lagard, V. / Jacobson, M.P. / Almo, S.C. / Gerlt, J.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4xfm.cif.gz | 237.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4xfm.ent.gz | 191 KB | Display | PDB format |
PDBx/mmJSON format | 4xfm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4xfm_validation.pdf.gz | 451 KB | Display | wwPDB validaton report |
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Full document | 4xfm_full_validation.pdf.gz | 454 KB | Display | |
Data in XML | 4xfm_validation.xml.gz | 20 KB | Display | |
Data in CIF | 4xfm_validation.cif.gz | 31 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xf/4xfm ftp://data.pdbj.org/pub/pdb/validation_reports/xf/4xfm | HTTPS FTP |
-Related structure data
Related structure data | 4xfrC 4xg0C 4xgjSC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | |
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 | biological unit is undetermined, could be monomer or dimer |
-Components
#1: Protein | Mass: 49278.484 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pectobacterium atrosepticum (bacteria) / Strain: SCRI 1043 / ATCC BAA-672 / Gene: ECA3761 / Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q6D0N7 |
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#2: Chemical | ChemComp-THE / |
#3: 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: 2.28 Å3/Da / Density % sol: 45.95 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: Protein (67.0 mg/ml, 10 mM HEPES pH 7.5, 5 mM DTT, 10 mM D-Threonate); Reservoir (MCSG1(F1); 0.1 M Bis-Tris pH 6.5, 20%(w/v) PEG MME 5000); Cryoprotection (80% Reservoir, 20% ethylene glycol) |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.9793 Å | |||||||||||||||||||||||||||
Detector | Type: RAYONIX MX225HE / Detector: CCD / Date: Jul 10, 2014 / Details: MIRRORS | |||||||||||||||||||||||||||
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9793 Å / Relative weight: 1 | |||||||||||||||||||||||||||
Reflection | Resolution: 1.55→61.3 Å / Num. obs: 63987 / % possible obs: 99 % / Redundancy: 3.7 % / Biso Wilson estimate: 19.92 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.049 / Rpim(I) all: 0.03 / Net I/σ(I): 14 / Num. measured all: 234457 / Scaling rejects: 10 | |||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Rejects: _
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4XGJ Resolution: 1.55→27.919 Å / FOM work R set: 0.8859 / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 18.59 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 99.48 Å2 / Biso mean: 30.56 Å2 / Biso min: 10.8 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.55→27.919 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 23
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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