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Yorodumi- PDB-2yio: Crystal Structure of Parasite Sarcocystis muris Microneme Protein... -
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-Basic information
Entry | Database: PDB / ID: 2yio | ||||||
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Title | Crystal Structure of Parasite Sarcocystis muris Microneme Protein SML- 2 in complex with 1-Thio-beta-D-Galactose (SPACEGROUP C2221) | ||||||
Components | MICRONEME ANTIGEN L2 | ||||||
Keywords | SUGAR BINDING PROTEIN / APPLE-DOMAIN TANDEM REPEAT / PAN_AP / PAN_1 / GALACTOSE-BINDING LECTIN / CELLULAR ADHESION / MICRONEMAL PROTEIN | ||||||
Function / homology | Function and homology information microneme / cytoplasmic vesicle / carbohydrate binding / cell adhesion / proteolysis / extracellular region Similarity search - Function | ||||||
Biological species | SARCOCYSTIS MURIS (eukaryote) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.43 Å | ||||||
Authors | Mueller, J.J. / Heinemann, U. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2011 Title: Pan-Modular Structure of Microneme Protein Sml-2 from Parasite Sarcocystis Muris at 1.95 A Resolution and its Complex with 1-Thio-Beta-D-Galactose. Authors: Mueller, J.J. / Weiss, M.S. / Heinemann, U. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2yio.cif.gz | 65.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2yio.ent.gz | 48.6 KB | Display | PDB format |
PDBx/mmJSON format | 2yio.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2yio_validation.pdf.gz | 475.3 KB | Display | wwPDB validaton report |
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Full document | 2yio_full_validation.pdf.gz | 476.8 KB | Display | |
Data in XML | 2yio_validation.xml.gz | 13.5 KB | Display | |
Data in CIF | 2yio_validation.cif.gz | 18 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yi/2yio ftp://data.pdbj.org/pub/pdb/validation_reports/yi/2yio | HTTPS FTP |
-Related structure data
Related structure data | 2yilSC 2yipC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: VAL / Beg label comp-ID: VAL / End auth comp-ID: TYR / End label comp-ID: TYR / Refine code: 5 / Auth seq-ID: 7 - 130 / Label seq-ID: 7 - 130
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-Components
-Protein / Sugars , 2 types, 4 molecules AB
#1: Protein | Mass: 15094.004 Da / Num. of mol.: 2 / Source method: isolated from a natural source Details: CYST MEROZOITES OF SARCOCYSTIS MURIS FROM SKELETAL MOUSE MUSCLES. Source: (natural) SARCOCYSTIS MURIS (eukaryote) / References: UniProt: P81860 #5: Sugar | |
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-Non-polymers , 4 types, 104 molecules
#2: Chemical | ChemComp-CL / #3: Chemical | #4: Chemical | #6: 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: 3.34 Å3/Da / Density % sol: 63.2 % / Description: NONE |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.9 Details: VAPOR DIFFUSION, HANGING DROP. PH 7.9, TEMPERATURE 291K. PROTEIN SOLUTION:50 MM TRIS-HCL, 150 MM NACL, PH 8.3, 12 MG/ML SML-2. RESERVOIR: 0.1 M HEPES, PH 7.5, 0.1 M NACL, 1.7 M AMMONIUM ...Details: VAPOR DIFFUSION, HANGING DROP. PH 7.9, TEMPERATURE 291K. PROTEIN SOLUTION:50 MM TRIS-HCL, 150 MM NACL, PH 8.3, 12 MG/ML SML-2. RESERVOIR: 0.1 M HEPES, PH 7.5, 0.1 M NACL, 1.7 M AMMONIUM SULFATE, 15% GLYCEROL. DROPLET: 1 MICROLITER PROTEIN SOLUTION: 1 MICROLITER RESERVOIR SOLUTION. PROTEIN:1-THIO-BETA-D-GALACTOSE, MOLAR RATIO 1:100. |
-Data collection
Diffraction | Mean temperature: 110 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU H2B / Wavelength: 1.542 |
Detector | Type: MARRESEARCH MAR30 / Detector: IMAGE PLATE / Date: May 5, 2000 / Details: GOEBEL MIRROR |
Radiation | Monochromator: MAXFLUX MIRROR OSMIC / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.542 Å / Relative weight: 1 |
Reflection | Resolution: 2.43→23.9 Å / Num. obs: 15317 / % possible obs: 99.1 % / Observed criterion σ(I): -3 / Redundancy: 5 % / Biso Wilson estimate: 30.2 Å2 / Rmerge(I) obs: 0.04 / Net I/σ(I): 29.1 |
Reflection shell | Resolution: 2.43→2.5 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.15 / Mean I/σ(I) obs: 8.44 / % possible all: 92.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2YIL Resolution: 2.43→23.83 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.919 / SU B: 5.768 / SU ML: 0.138 / Cross valid method: THROUGHOUT / ESU R: 0.25 / ESU R Free: 0.202 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY.
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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: 36.229 Å2
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Refinement step | Cycle: LAST / Resolution: 2.43→23.83 Å
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Refine LS restraints |
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