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Yorodumi- PDB-6dcm: The atomic resolution crystal structure of Kringle 2 variant boun... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6dcm | |||||||||
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Title | The atomic resolution crystal structure of Kringle 2 variant bound with EACA | |||||||||
Components | PlasminogenPlasmin | |||||||||
Keywords | BLOOD CLOTTING / Kringle 2 | |||||||||
Function / homology | Plasminogen Kringle 4 / Plasminogen Kringle 4 / Beta Barrel / Mainly Beta / 6-AMINOHEXANOIC ACID Function and homology information | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.031 Å | |||||||||
Authors | Ghanbarpour, A. / Geiger, J. | |||||||||
Citation | Journal: To Be Published Title: The atomic resolution crystal structure of Kringle 2 variant bound with EACA Authors: Ghanbarpour, A. / Geiger, J. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6dcm.cif.gz | 51.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6dcm.ent.gz | 35.2 KB | Display | PDB format |
PDBx/mmJSON format | 6dcm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dc/6dcm ftp://data.pdbj.org/pub/pdb/validation_reports/dc/6dcm | HTTPS FTP |
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-Related structure data
Related structure data | 1i5kS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 9801.812 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PLG / Production host: Komagataella pastoris (fungus) / References: plasmin |
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#2: Chemical | ChemComp-ACA / |
#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: 1.78 Å3/Da / Density % sol: 30.91 % |
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Crystal grow | Temperature: 298 K / Method: evaporation / Details: PEG 4000, Sodium acetate, Ammonium acetate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 0.987 Å |
Detector | Type: RAYONIX MX300HE / Detector: CCD / Date: Feb 14, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.987 Å / Relative weight: 1 |
Reflection | Resolution: 1.031→23.46 Å / Num. obs: 31093 / % possible obs: 98.8 % / Redundancy: 4 % / Rmerge(I) obs: 0.062 / Rrim(I) all: 0.07 / Net I/av σ(I): 34.5 / Net I/σ(I): 34.5 |
Reflection shell | Resolution: 1.031→1.068 Å / Rmerge(I) obs: 0.368 / Mean I/σ(I) obs: 4.7 / Rrim(I) all: 0.447 / % possible all: 99.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1I5K Resolution: 1.031→23.458 Å / SU ML: 0.12 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 15.59
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.031→23.458 Å
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Refine LS restraints |
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LS refinement shell |
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