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Open data
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Basic information
Entry | Database: PDB / ID: 2hlc | ||||||
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Title | HL COLLAGENASE STRUCTURE AT 1.7A RESOLUTION | ||||||
![]() | COLLAGENASE | ||||||
![]() | SERINE PROTEASE / HYDROLASE / COLLAGEN DEGRADATION | ||||||
Function / homology | ![]() hypodermin C / collagen catabolic process / serine-type endopeptidase activity / proteolysis / extracellular region Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Broutin, I. / Merigeau, K. / Arnoux, B. / Ducruix, A. | ||||||
![]() | ![]() Title: 1.8 A structure of Hypoderma lineatum collagenase: a member of the serine proteinase family. Authors: Broutin, I. / Arnoux, B. / Riche, C. / Lecroisey, A. / Keil, B. / Pascard, C. / Ducruix, A. #1: ![]() Title: Collagenase-Collagenase Interactions, a Descriptor for the Mapping of the Binding Site Authors: Broutin, I. / Merigeau, K. / Arnoux, B. / Ducruix, A. #2: ![]() Title: Crystallographic Analyses of Lysozyme and Collagenase Space Grown Crystals Versus Ground Controls Authors: Broutin, I. / Ries-Kautt, M. / Ducruix, A. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 101.6 KB | Display | ![]() |
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PDB format | ![]() | 81.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 416.1 KB | Display | ![]() |
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Full document | ![]() | 419.5 KB | Display | |
Data in XML | ![]() | 21.8 KB | Display | |
Data in CIF | ![]() | 31.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1hylSC S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 25247.189 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() References: UniProt: P08897, Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.54 Å3/Da / Density % sol: 50 % | ||||||||||||||||||||||||||||||
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Crystal grow | Method: vapor diffusion - hanging drop in microgravity / pH: 7 Details: PROTEIN CONCENTRATION WAS 10MG/ML. IT WAS CRYSTALLIZED IN 1.4M AMMONIUM SULFATE BY HANGING DROP METHOD IN APCF REACTORS UNDER MICROGRAVITY (IML2 MISSION)., pH 7.0, vapor diffusion - hanging drop in microgravity | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 291 K / Method: microdialysis / Details: or vapor diffusion | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 280 K |
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Diffraction source | Source: ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Nov 1, 1995 |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9375 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→15 Å / Num. obs: 54909 / % possible obs: 96.3 % / Observed criterion σ(I): 0 / Redundancy: 4.4 % / Biso Wilson estimate: 23.18 Å2 / Rsym value: 0.047 / Net I/σ(I): 11.4 |
Reflection shell | Resolution: 1.7→1.74 Å / Redundancy: 3.8 % / Mean I/σ(I) obs: 1.6 / Rsym value: 0.478 / % possible all: 99.6 |
Reflection | *PLUS Rmerge(I) obs: 0.047 |
Reflection shell | *PLUS % possible obs: 99.6 % / Rmerge(I) obs: 0.478 |
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Processing
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Refinement | Method to determine structure: RIGID BODY Starting model: PDB ENTRY 1HYL Resolution: 1.7→8 Å / Cross valid method: THROUGHOUT
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Displacement parameters | Biso mean: 22.6 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.23 Å / Luzzati d res low obs: 8 Å / Luzzati sigma a obs: 0.21 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.7→8 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.7→1.78 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: 0.3428 |