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Open data
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Basic information
Entry | Database: PDB / ID: 1fdp | ||||||
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Title | PROENZYME OF HUMAN COMPLEMENT FACTOR D, RECOMBINANT PROFACTOR D | ||||||
![]() | PROENZYME OF COMPLEMENT FACTOR D | ||||||
![]() | HYDROLASE / SERINE PROTEASE / COMPLEMENT / FACTOR D / PROFACTOR D / ZYMOGEN / PROENZYME | ||||||
Function / homology | ![]() 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 | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Jing, H. / Macon, K.J. / Moore, D. / Delucas, L.J. / Volanakis, J.E. / Narayana, S.V.L. | ||||||
![]() | ![]() Title: Structural basis of profactor D activation: from a highly flexible zymogen to a novel self-inhibited serine protease, complement factor D. Authors: Jing, H. / Macon, K.J. / Moore, D. / DeLucas, L.J. / Volanakis, J.E. / Narayana, S.V. #1: ![]() 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.L. #2: ![]() Title: Complement Factor D, a Novel Serine Protease Authors: Volanakis, J.E. / Narayana, S.V.L. #3: ![]() Title: Structure of Human Factor D. A Complement System Protein at 2.0 A Resolution Authors: Narayana, S.V.L. / Carson, M. / El-Kabbani, O. / Kilpatrick, J.M. / Moore, D. / Chen, X. / Bugg, C.E. / Volanakis, J.E. / Delucas, L.J. #4: ![]() Title: Preliminary Crystallographic Studies on Human Complement Profactor D Authors: Narayana, S.V.L. / Yamauchi, Y. / Macon, K.J. / Moore, D. / Delucas, L.J. / Volanakis, J.E. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 177.6 KB | Display | ![]() |
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PDB format | ![]() | 140.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 460.1 KB | Display | ![]() |
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Full document | ![]() | 485.6 KB | Display | |
Data in XML | ![]() | 40 KB | Display | |
Data in CIF | ![]() | 57.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1dsuS 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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2 | ![]()
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3 | ![]()
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4 | ![]()
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper:
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Components
#1: Protein | Mass: 25146.633 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Water | ChemComp-HOH / | Sequence details | CHYMOTRYPS | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.9 Å3/Da / Density % sol: 36 % | ||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.2 Details: CRYSTALLIZATION CONDITIONS: THE RESERVOIR SOLUTION CONTAINED 10-12% PEG-6000 AND 30MM MES (PH5.2). THE DROPS CONTAINED EQUAL VOLUME OF RESERVOIR SOLUTION AND PROTEIN SOLUTION (10MG/ML), ...Details: CRYSTALLIZATION CONDITIONS: THE RESERVOIR SOLUTION CONTAINED 10-12% PEG-6000 AND 30MM MES (PH5.2). THE DROPS CONTAINED EQUAL VOLUME OF RESERVOIR SOLUTION AND PROTEIN SOLUTION (10MG/ML), VAPOR DIFFUSION, HANGING DROP, temperature 298K | ||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 7 / Method: vapor diffusion, sitting drop | ||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 95 K |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Feb 1, 1997 / Details: COLLIMATOR |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→30 Å / Num. obs: 43713 / % possible obs: 98.5 % / Observed criterion σ(I): 0 / Redundancy: 2.5 % / Biso Wilson estimate: 22.8 Å2 / Rmerge(I) obs: 0.066 / Net I/σ(I): 13.8 |
Reflection shell | Resolution: 2.1→2.18 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.234 / Mean I/σ(I) obs: 3.9 / % possible all: 96.8 |
Reflection | *PLUS Num. measured all: 93825 |
Reflection shell | *PLUS % possible obs: 96.8 % |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: CORE REGION OF FACTOR D (1DSU MOLECULE B) Resolution: 2.1→30 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 1000000 / Data cutoff low absF: 0.001 / Cross valid method: THROUGHOUT / σ(F): 0 / Details: BULK SOLVENT CORRECTION WAS APPLIED
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Displacement parameters | Biso mean: 24.5 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.1→30 Å
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Refine LS restraints |
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Refine LS restraints NCS | NCS model details: RESTRAINED WITH NCS AVERAGE PHASES | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.1→2.2 Å / Rfactor Rfree error: 0.01 / Total num. of bins used: 8
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Xplor file |
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Software | *PLUS Name: ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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