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Yorodumi- PDB-1bio: HUMAN COMPLEMENT FACTOR D IN COMPLEX WITH ISATOIC ANHYDRIDE INHIBITOR -
+Open data
-Basic information
Entry | Database: PDB / ID: 1bio | ||||||
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Title | HUMAN COMPLEMENT FACTOR D IN COMPLEX WITH ISATOIC ANHYDRIDE INHIBITOR | ||||||
Components | COMPLEMENT FACTOR D | ||||||
Keywords | SERINE PROTEASE / HYDROLASE / COMPLEMENT / FACTOR D / CATALYTIC TRIAD / SELF-REGULATION | ||||||
Function / homology | Function and homology information complement factor D / Alternative complement activation / complement activation, alternative pathway / complement activation / serine-type peptidase activity / platelet alpha granule lumen / response to bacterium / Platelet degranulation / secretory granule lumen / ficolin-1-rich granule lumen ...complement factor D / Alternative complement activation / complement activation, alternative pathway / complement activation / serine-type peptidase activity / platelet alpha granule lumen / response to bacterium / Platelet degranulation / secretory granule lumen / ficolin-1-rich granule lumen / serine-type endopeptidase activity / Neutrophil degranulation / proteolysis / extracellular exosome / extracellular region Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.5 Å | ||||||
Authors | Jing, H. / Babu, Y.S. / Moore, D. / Kilpatrick, J.M. / Liu, X.-Y. / Volanakis, J.E. / Narayana, S.V.L. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 1998 Title: Structures of native and complexed complement factor D: implications of the atypical His57 conformation and self-inhibitory loop in the regulation of specific serine protease activity. Authors: Jing, H. / Babu, Y.S. / Moore, D. / Kilpatrick, J.M. / Liu, X.Y. / Volanakis, J.E. / Narayana, S.V. #1: Journal: Protein Sci. / Year: 1996 Title: Complement Factor D, a Novel Serine Protease Authors: Volanakis, J.E. / Narayana, S.V. #2: Journal: J.Biol.Chem. / Year: 1995 Title: Crystal Structure of a Complement Factor D Mutant Expressing Enhanced Catalytic Activity Authors: Kim, S. / Narayana, S.V. / Volanakis, J.E. #3: Journal: J.Biol.Chem. / Year: 1995 Title: Erratum. Crystal Structure of a Complement Factor D Mutant Expressing Enhanced Catalytic Activity Authors: Kim, S. / Narayana, S.V. / Volanakis, J.E. #4: Journal: J.Mol.Biol. / Year: 1994 Title: Structure of Human Factor D. A Complement System Protein at 2.0 A Resolution Authors: Narayana, S.V. / Carson, M. / El-Kabbani, O. / Kilpatrick, J.M. / Moore, D. / Chen, X. / Bugg, C.E. / Volanakis, J.E. / Delucas, L.J. #5: Journal: J.Mol.Biol. / Year: 1991 Title: Crystallization and Preliminary X-Ray Investigation of Factor D of Human Complement Authors: Narayana, S.V. / Kilpatrick, J.M. / El-Kabbani, O. / Babu, Y.S. / Bugg, C.E. / Volanakis, J.E. / Delucas, L.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1bio.cif.gz | 59.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1bio.ent.gz | 45.2 KB | Display | PDB format |
PDBx/mmJSON format | 1bio.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1bio_validation.pdf.gz | 446.7 KB | Display | wwPDB validaton report |
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Full document | 1bio_full_validation.pdf.gz | 449.1 KB | Display | |
Data in XML | 1bio_validation.xml.gz | 14 KB | Display | |
Data in CIF | 1bio_validation.cif.gz | 21 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bi/1bio ftp://data.pdbj.org/pub/pdb/validation_reports/bi/1bio | HTTPS FTP |
-Related structure data
Related structure data | 1hfdC 1dsuS 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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Unit cell |
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-Components
#1: Protein | Mass: 24438.807 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: ISATOIC ANHYDRIDE ACYLATES ACTIVE SITE SER 195 / Source: (natural) Homo sapiens (human) / References: UniProt: P00746, complement factor D |
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#2: Chemical | ChemComp-SOA / |
#3: Chemical | ChemComp-GOL / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 2 |
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-Sample preparation
Crystal | Density Matthews: 2.15 Å3/Da / Density % sol: 44 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 6.4 / Details: pH 6.4 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, hanging dropDetails: drop consists of equal volume of protein and reservoir solutions | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 95 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418 |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jan 1, 1997 / Details: MIRRORS |
Radiation | Monochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→20 Å / Num. obs: 31552 / % possible obs: 95 % / Observed criterion σ(I): 2 / Redundancy: 4.1 % / Biso Wilson estimate: 17.8 Å2 / Rmerge(I) obs: 0.051 / Net I/σ(I): 29 |
Reflection shell | Resolution: 1.5→1.55 Å / Redundancy: 4 % / Rmerge(I) obs: 0.253 / Mean I/σ(I) obs: 5.5 / % possible all: 90 |
Reflection | *PLUS Num. measured all: 133846 |
Reflection shell | *PLUS % possible obs: 90 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1DSU MOLECULE B Resolution: 1.5→20 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 1000000 / Data cutoff low absF: 0.001 / Cross valid method: THROUGHOUT / σ(F): 2 / Details: BULK SOLVENT CORRECTION WAS APPLIED
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Displacement parameters | Biso mean: 17.3 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.5→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.5→1.57 Å / Rfactor Rfree error: 0.017 / Total num. of bins used: 8
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Xplor file |
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Software | *PLUS Name: X-PLOR / Version: 3.851 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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