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Yorodumi- PDB-3d5h: Crystal structure of haementhin from Haemanthus multiflorus at 2.... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3d5h | ||||||
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Title | Crystal structure of haementhin from Haemanthus multiflorus at 2.0A resolution: Formation of a novel loop on a TIM barrel fold and its functional significance | ||||||
Components | Haementhin | ||||||
Keywords | PROTEIN BINDING / TIM barrel | ||||||
Function / homology | Function and homology information alpha-amylase inhibitor activity / chitinase activity / carbohydrate metabolic process / extracellular region Similarity search - Function | ||||||
Biological species | Scadoxus multiflorus (plant) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Kumar, S. / Singh, N. / Sinha, M. / Singh, S.B. / Bhushan, A. / Kaur, P. / Srinivasan, A. / Sharma, S. / Singh, T.P. | ||||||
Citation | Journal: To be Published Title: Crystal structure of haementhin from Haemanthus multiflorus at 2.0A resolution: Formation of a novel loop on a TIM barrel fold and its functional significance Authors: Kumar, S. / Singh, N. / Sinha, M. / Singh, S.B. / Bhushan, A. / Kaur, P. / Srinivasan, A. / Sharma, S. / Singh, T.P. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3d5h.cif.gz | 73.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3d5h.ent.gz | 53 KB | Display | PDB format |
PDBx/mmJSON format | 3d5h.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3d5h_validation.pdf.gz | 444.4 KB | Display | wwPDB validaton report |
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Full document | 3d5h_full_validation.pdf.gz | 450.1 KB | Display | |
Data in XML | 3d5h_validation.xml.gz | 16 KB | Display | |
Data in CIF | 3d5h_validation.cif.gz | 23.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/d5/3d5h ftp://data.pdbj.org/pub/pdb/validation_reports/d5/3d5h | HTTPS FTP |
-Related structure data
Related structure data | 2hvmS 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: 29818.389 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Scadoxus multiflorus (plant) / References: UniProt: B2ZGS7 |
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#2: Chemical | ChemComp-ACT / |
#3: Chemical | ChemComp-PO4 / |
#4: 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: 2.27 Å3/Da / Density % sol: 45.81 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.2 Details: 0.1M ammonium sulphate, 20% PEG 6000, 0.1M sodium acetate, 20mM phosphate buffer, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 293 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.54132 Å |
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Oct 15, 2007 / Details: Mirror |
Radiation | Monochromator: Graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54132 Å / Relative weight: 1 |
Reflection | Resolution: 2→48.224 Å / Num. all: 18131 / Num. obs: 16787 / % possible obs: 97.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 |
Reflection shell | Resolution: 2→2.05 Å / % possible all: 97.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2HVM Resolution: 2→48.22 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.947 / SU B: 3.928 / SU ML: 0.109 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.181 / ESU R Free: 0.145 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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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: 26.53 Å2
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Refinement step | Cycle: LAST / Resolution: 2→48.22 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.052 Å / Total num. of bins used: 20 /
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