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- PDB-1bik: X-RAY STRUCTURE OF BIKUNIN FROM THE HUMAN INTER-ALPHA-INHIBITOR C... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1bik | ||||||
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Title | X-RAY STRUCTURE OF BIKUNIN FROM THE HUMAN INTER-ALPHA-INHIBITOR COMPLEX | ||||||
![]() | BIKUNIN | ||||||
![]() | GLYCOPROTEIN / BIKUNIN / TRYPSTATIN / URINARY TRYPSIN INHIBITOR / URONIC-ACID-RICH PROTEIN / SERINE PROTEASE INHIBITOR (KUNITZ TYPE) / GLYCOSYLATED PROTEIN | ||||||
Function / homology | ![]() 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 / nuclear membrane / collagen-containing extracellular matrix / 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 | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Xu, Y. / Carr, P.D. / Guss, J.M. / Ollis, D.L. | ||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 31 KB | Display | ![]() |
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PDB format | ![]() | 22.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | 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 |
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Links
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Assembly
Deposited unit | ![]()
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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) ![]() | ||
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#2: Sugar | ChemComp-NAG / | ||
#3: Chemical | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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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: ![]() |
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 % |
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Processing
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Refinement | Method to determine structure: ![]() 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: ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor obs: 0.29 |