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Yorodumi- PDB-1bik: X-RAY STRUCTURE OF BIKUNIN FROM THE HUMAN INTER-ALPHA-INHIBITOR C... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1bik | ||||||
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Title | X-RAY STRUCTURE OF BIKUNIN FROM THE HUMAN INTER-ALPHA-INHIBITOR COMPLEX | ||||||
Components | BIKUNINAlpha-1-microglobulin/bikunin precursor | ||||||
Keywords | GLYCOPROTEIN / BIKUNIN / TRYPSTATIN / URINARY TRYPSIN INHIBITOR / URONIC-ACID-RICH PROTEIN / SERINE PROTEASE INHIBITOR (KUNITZ TYPE) / GLYCOSYLATED PROTEIN | ||||||
Function / homology | Function and homology information Oxidoreductases; Acting on NADH or NADPH; With a heme protein as acceptor / calcium oxalate binding / IgA binding / heme catabolic process / negative regulation of immune response / negative regulation of JNK cascade / calcium channel inhibitor activity / Scavenging of heme from plasma / female pregnancy / serine-type endopeptidase inhibitor activity ...Oxidoreductases; Acting on NADH or NADPH; With a heme protein as acceptor / calcium oxalate binding / IgA binding / heme catabolic process / negative regulation of immune response / negative regulation of JNK cascade / calcium channel inhibitor activity / Scavenging of heme from plasma / female pregnancy / serine-type endopeptidase inhibitor activity / carbohydrate binding / collagen-containing extracellular matrix / nuclear membrane / blood microparticle / mitochondrial inner membrane / oxidoreductase activity / cell adhesion / heme binding / cell surface / endoplasmic reticulum / protein homodimerization activity / extracellular space / extracellular exosome / extracellular region / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.5 Å | ||||||
Authors | Xu, Y. / Carr, P.D. / Guss, J.M. / Ollis, D.L. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 1998 Title: The crystal structure of bikunin from the inter-alpha-inhibitor complex: a serine protease inhibitor with two Kunitz domains. Authors: Xu, Y. / Carr, P.D. / Guss, J.M. / Ollis, D.L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1bik.cif.gz | 31 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1bik.ent.gz | 22.7 KB | Display | PDB format |
PDBx/mmJSON format | 1bik.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bi/1bik ftp://data.pdbj.org/pub/pdb/validation_reports/bi/1bik | HTTPS FTP |
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-Related structure data
Related structure data | 1kntS 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: 15987.002 Da / Num. of mol.: 1 / Fragment: DOMAIN II,78 - 133 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Secretion: URINE / References: UniProt: P02760 | ||
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#2: Sugar | ChemComp-NAG / | ||
#3: Chemical | #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: 3.51 Å3/Da / Density % sol: 64.97 % Description: NON IDENTICAL RESIDUES TRUNCATED TO THE CB POSITION | |||||||||||||||||||||||||
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Crystal grow | pH: 7.5 / Details: pH 7.5 | |||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, hanging drop | |||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 293 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418 |
Detector | Type: RIGAKU RAXIS II / Detector: IMAGE PLATE / Date: Nov 1, 1995 / Details: COLLIMATOR |
Radiation | Monochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→25 Å / Num. obs: 8519 / % possible obs: 97.7 % / Redundancy: 6.5 % / Rmerge(I) obs: 0.072 / Net I/σ(I): 13.4 |
Reflection shell | Resolution: 2.5→2.6 Å / Redundancy: 6 % / Rmerge(I) obs: 0.21 / Mean I/σ(I) obs: 10.1 / % possible all: 97.6 |
Reflection | *PLUS Num. measured all: 55165 |
Reflection shell | *PLUS % possible obs: 97.6 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: C-TERMINAL DOMAIN OF PDB ENTRY 1KNT Resolution: 2.5→8 Å / Cross valid method: THROUGHOUT / σ(F): 2
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Refinement step | Cycle: LAST / Resolution: 2.5→8 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.5→2.6 Å / Total num. of bins used: 8
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Xplor file |
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Software | *PLUS Name: X-PLOR / Version: 3.1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor obs: 0.29 |