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Yorodumi- PDB-1hfc: 1.56 ANGSTROM STRUCTURE OF MATURE TRUNCATED HUMAN FIBROBLAST COLL... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1hfc | ||||||
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Title | 1.56 ANGSTROM STRUCTURE OF MATURE TRUNCATED HUMAN FIBROBLAST COLLAGENASE | ||||||
Components | FIBROBLAST COLLAGENASE | ||||||
Keywords | METALLOPROTEASE | ||||||
Function / homology | Function and homology information interstitial collagenase / cellular response to UV-A / protein metabolic process / Basigin interactions / Activation of Matrix Metalloproteinases / Collagen degradation / collagen catabolic process / extracellular matrix disassembly / Degradation of the extracellular matrix / extracellular matrix ...interstitial collagenase / cellular response to UV-A / protein metabolic process / Basigin interactions / Activation of Matrix Metalloproteinases / Collagen degradation / collagen catabolic process / extracellular matrix disassembly / Degradation of the extracellular matrix / extracellular matrix / extracellular matrix organization / positive regulation of protein-containing complex assembly / metalloendopeptidase activity / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / peptidase activity / endopeptidase activity / Interleukin-4 and Interleukin-13 signaling / serine-type endopeptidase activity / proteolysis / extracellular space / zinc ion binding / extracellular region Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / Resolution: 1.5 Å | ||||||
Authors | Spurlino, J.C. / Smith, D.L. | ||||||
Citation | Journal: Proteins / Year: 1994 Title: 1.56 A structure of mature truncated human fibroblast collagenase. Authors: Spurlino, J.C. / Smallwood, A.M. / Carlton, D.D. / Banks, T.M. / Vavra, K.J. / Johnson, J.S. / Cook, E.R. / Falvo, J. / Wahl, R.C. / Pulvino, T.A. / Wendoloski, J.J. / Smith, D.L. #1: Journal: Nat.Struct.Biol. / Year: 1994 Title: Structure of Human Neutrophil Collagenase Reveals Large S1' Specificity Pocket Authors: Stams, T. / Spurlino, J.C. / Smith, D.L. / Wahl, R.C. / Ho, T.F. / Qoronfleh, M.W. / Banks, T.M. / Rubin, B. | ||||||
History |
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Remark 700 | SHEET S1 AS PRESENTED ON SHEET RECORDS BELOW IS A FIVE-STRANDED SHEET. THE HET GROUP HAP IS LOCATED ...SHEET S1 AS PRESENTED ON SHEET RECORDS BELOW IS A FIVE-STRANDED SHEET. THE HET GROUP HAP IS LOCATED IN SUCH A POSITION THAT IT COULD BE CONSIDERED THE SIXTH STRAND OF THIS SHEET SHEET AND PRO 238 - PHE 242 COULD BE CONSIDERED THE SEVENTH STRAND OF THIS SHEET. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1hfc.cif.gz | 48 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1hfc.ent.gz | 32.8 KB | Display | PDB format |
PDBx/mmJSON format | 1hfc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1hfc_validation.pdf.gz | 448 KB | Display | wwPDB validaton report |
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Full document | 1hfc_full_validation.pdf.gz | 455.6 KB | Display | |
Data in XML | 1hfc_validation.xml.gz | 6.1 KB | Display | |
Data in CIF | 1hfc_validation.cif.gz | 8.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hf/1hfc ftp://data.pdbj.org/pub/pdb/validation_reports/hf/1hfc | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Atom site foot note | 1: RESIDUES GLU 209 AND TYR 210 FORM A CIS-PEPTIDE BOND. |
-Components
#1: Protein | Mass: 18865.541 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / References: UniProt: P03956, interstitial collagenase | ||||||
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#2: Chemical | #3: Chemical | ChemComp-CA / | #4: Chemical | ChemComp-PLH / | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.34 Å3/Da / Density % sol: 47.41 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | *PLUS pH: 7.5 / Method: batch method | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Radiation | Scattering type: x-ray |
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Radiation wavelength | Relative weight: 1 |
Reflection | *PLUS Highest resolution: 1.56 Å / Lowest resolution: 2.83 Å / Num. obs: 23912 / % possible obs: 89.7 % / Num. measured all: 64262 / Rmerge(I) obs: 0.0642 |
Reflection shell | *PLUS Highest resolution: 1.56 Å / Lowest resolution: 1.66 Å / % possible obs: 73.7 % / Num. unique obs: 3218 / Num. measured obs: 5791 / Rmerge(I) obs: 0.2688 |
-Processing
Software |
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Refinement | Resolution: 1.5→10 Å / σ(F): 2 /
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Refinement step | Cycle: LAST / Resolution: 1.5→10 Å
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Refine LS restraints |
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Software | *PLUS Name: X-PLOR/PROLSQ / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 1.56 Å / Rfactor obs: 0.174 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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