+Open data
-Basic information
Entry | Database: PDB / ID: 1b1u | |||||||||
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Title | CRYSTAL STRUCTURE OF THE BIFUNCTIONAL INHIBITOR RAGI | |||||||||
Components | PROTEIN (ALPHA-AMYLASE/TRYPSIN INHIBITOR RATI) | |||||||||
Keywords | HYDROLASE INHIBITOR / ALPHA-AMYLASE/TRYPSIN INHIBITOR (RATI) / BIFUNCTIONAL | |||||||||
Function / homology | Function and homology information alpha-amylase inhibitor activity / serine-type endopeptidase inhibitor activity / extracellular region Similarity search - Function | |||||||||
Biological species | Eleusine coracana (finger millet) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | |||||||||
Authors | Gourinath, S. / Srinivasan, A. / Singh, T.P. | |||||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2000 Title: Structure of the bifunctional inhibitor of trypsin and alpha-amylase from ragi seeds at 2.2 A resolution. Authors: Gourinath, S. / Alam, N. / Srinivasan, A. / Betzel, C. / Singh, T.P. #1: Journal: Biochemistry / Year: 1995 Title: Determination of the Three-Dimensional Structure of the Bifunctional Alpha-Amylase/Trypsin Inhibitor from Ragi Seeds by NMR Spectroscopy Authors: Strobl, S. / Muhlhahn, P. / Bernstein, R. / Wiltscheck, R. / Maskos, K. / Wunderlich, M. / Huber, R. / Glockshuber, R. / Holak, T.A. #2: Journal: J.Mol.Biol. / Year: 1991 Title: Preliminary X-Ray Investigation of a Bifunctional Inhibitor from Indian Finger Millet (Ragi) Authors: Srinivasan, A. / Raman, A. / Singh, T.P. #3: Journal: FEBS Lett. / Year: 1983 Title: The Complete Amino Acid Sequence of the Bifunctional Alpha-Amylase/Trypsin Inhibitor from Seeds of Ragi (Indian Finger Millet, Eleusine Coracana Gaertn.) Authors: Campos, F.A.P. / Richardson, M. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1b1u.cif.gz | 36.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1b1u.ent.gz | 24.2 KB | Display | PDB format |
PDBx/mmJSON format | 1b1u.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1b1u_validation.pdf.gz | 362.2 KB | Display | wwPDB validaton report |
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Full document | 1b1u_full_validation.pdf.gz | 370.6 KB | Display | |
Data in XML | 1b1u_validation.xml.gz | 4.8 KB | Display | |
Data in CIF | 1b1u_validation.cif.gz | 6.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/b1/1b1u ftp://data.pdbj.org/pub/pdb/validation_reports/b1/1b1u | HTTPS FTP |
-Related structure data
Related structure data | 1bipS 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: 13153.313 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Eleusine coracana (finger millet) / Organ: SEED / References: UniProt: P01087 |
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#2: 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: 1.96 Å3/Da / Density % sol: 37.2 % | ||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 8 Details: 1.15M AMMONIUM SULFATE, 0.2M AMMONIUM PHOSPHATE PH 8.0 | ||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: microdialysis | ||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 173 K |
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Diffraction source | Source: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X31 / Wavelength: 1 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Jun 23, 1998 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→20 Å / Num. obs: 5684 / % possible obs: 98.7 % / Redundancy: 12.2 % / Biso Wilson estimate: 25.4 Å2 / Rsym value: 0.094 / Net I/σ(I): 11.2 |
Reflection shell | Resolution: 2.2→2.28 Å / Redundancy: 4.2 % / Mean I/σ(I) obs: 2.27 / Rsym value: 0.299 / % possible all: 94.6 |
Reflection | *PLUS Highest resolution: 2.2 Å / Lowest resolution: 10 Å / Num. obs: 5094 / % possible obs: 91 % / Num. measured all: 57852 / Rmerge(I) obs: 0.072 |
Reflection shell | *PLUS Highest resolution: 2.7 Å / Lowest resolution: 2.79 Å / % possible obs: 83.5 % / Redundancy: 4.2 % / Rmerge(I) obs: 0.162 / Mean I/σ(I) obs: 2.27 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1BIP, MODEL 20 Resolution: 2.2→10 Å / Rfactor Rfree error: 0.023 / Data cutoff high absF: 100000 / Data cutoff low absF: 0.1 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 1
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Displacement parameters | Biso mean: 24.8 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.3 Å / Luzzati d res low obs: 10 Å / Luzzati sigma a obs: 0.35 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.2→10 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.2→2.34 Å / Rfactor Rfree error: 0.083 / Total num. of bins used: 6
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Xplor file |
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Software | *PLUS Name: X-PLOR / Version: 3.851 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Num. reflection obs: 5094 / Rfactor all: 0.224 / Rfactor obs: 0.219 / Rfactor Rfree: 0.277 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Highest resolution: 2.2 Å |