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Yorodumi- PDB-3mli: 2ouf-ds, a disulfide-linked dimer of Helicobacter pylori protein ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3mli | ||||||
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Title | 2ouf-ds, a disulfide-linked dimer of Helicobacter pylori protein HP0242 | ||||||
Components | Putative uncharacterized protein | ||||||
Keywords | UNKNOWN FUNCTION / unknotted control | ||||||
Function / homology | HP0242-like domain / HP0242-like fold / Protein of unknown function DUF2018 / HP0242-like superfamily / Domain of unknown function (DUF2018) / Orthogonal Bundle / Mainly Alpha / metal ion binding / DUF2018 family protein Function and homology information | ||||||
Biological species | Helicobacter pylori (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.9 Å | ||||||
Authors | King, N.P. / Sawaya, M.R. / Jacobitz, A.W. / Yeates, T.O. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2010 Title: Structure and folding of a designed knotted protein. Authors: King, N.P. / Jacobitz, A.W. / Sawaya, M.R. / Goldschmidt, L. / Yeates, T.O. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3mli.cif.gz | 155.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3mli.ent.gz | 123.1 KB | Display | PDB format |
PDBx/mmJSON format | 3mli.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3mli_validation.pdf.gz | 461 KB | Display | wwPDB validaton report |
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Full document | 3mli_full_validation.pdf.gz | 464.9 KB | Display | |
Data in XML | 3mli_validation.xml.gz | 13.6 KB | Display | |
Data in CIF | 3mli_validation.cif.gz | 18.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ml/3mli ftp://data.pdbj.org/pub/pdb/validation_reports/ml/3mli | HTTPS FTP |
-Related structure data
Related structure data | 3mlgC 2ouf C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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-Components
#1: Protein | Mass: 11919.561 Da / Num. of mol.: 4 / Mutation: CYS44LEU, LEU93ASN Source method: isolated from a genetically manipulated source Details: The designed gene is a mutant of the Helicobacter pylori gene HP0242 Source: (gene. exp.) Helicobacter pylori (bacteria) / Gene: HP_0242 / Plasmid: pET22b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O25025 #2: Chemical | #3: 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: 2.36 Å3/Da / Density % sol: 47.79 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6 Details: 8.3% 2-propanol, 0.1 M MES pH 6.0, 0.32 M calcium acetate, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU FR-E SUPERBRIGHT / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS HTC / Detector: IMAGE PLATE / Date: Jan 5, 2010 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→80 Å / Num. all: 11588 / Num. obs: 11588 / % possible obs: 98.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 13.2 % / Rmerge(I) obs: 0.096 / Χ2: 1.077 / Net I/σ(I): 17.6 |
Reflection shell | Resolution: 2.9→3.02 Å / Redundancy: 13.7 % / Rmerge(I) obs: 0.537 / Num. unique all: 1136 / Χ2: 1.355 / % possible all: 98.3 |
-Phasing
Phasing | Method: molecular replacement | |||||||||
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Phasing MR | Model details: Phaser MODE: MR_AUTO
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2OUF 2ouf Resolution: 2.9→50.16 Å / Cor.coef. Fo:Fc: 0.93 / Cor.coef. Fo:Fc free: 0.927 / Occupancy max: 1 / Occupancy min: 1 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso max: 205.4 Å2 / Biso mean: 109.992 Å2 / Biso min: 45.39 Å2
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Refine analyze | Luzzati coordinate error obs: 0.683 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.9→50.16 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.9→3.24 Å / Total num. of bins used: 5
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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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