+Open data
-Basic information
Entry | Database: PDB / ID: 1gen | ||||||
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Title | C-TERMINAL DOMAIN OF GELATINASE A | ||||||
Components | GELATINASE A | ||||||
Keywords | HYDROLASE (METALLOPROTEASE) / HYDROLASE / HEMOPEXIN DOMAIN / METALLOPROTEASE | ||||||
Function / homology | Function and homology information gelatinase A / peripheral nervous system axon regeneration / blood vessel maturation / parturition / luteinization / bone trabecula formation / tissue remodeling / intramembranous ossification / cellular response to UV-A / ovulation from ovarian follicle ...gelatinase A / peripheral nervous system axon regeneration / blood vessel maturation / parturition / luteinization / bone trabecula formation / tissue remodeling / intramembranous ossification / cellular response to UV-A / ovulation from ovarian follicle / positive regulation of oxidative stress-induced neuron intrinsic apoptotic signaling pathway / prostate gland epithelium morphogenesis / protein metabolic process / cellular response to fluid shear stress / negative regulation of cell adhesion / face morphogenesis / negative regulation of vasoconstriction / endodermal cell differentiation / Activation of Matrix Metalloproteinases / macrophage chemotaxis / response to amyloid-beta / fibronectin binding / Collagen degradation / collagen catabolic process / EPH-ephrin mediated repulsion of cells / extracellular matrix disassembly / response to hyperoxia / ephrin receptor signaling pathway / cellular response to interleukin-1 / response to electrical stimulus / response to mechanical stimulus / response to retinoic acid / ovarian follicle development / positive regulation of vascular associated smooth muscle cell proliferation / embryo implantation / Degradation of the extracellular matrix / sarcomere / extracellular matrix organization / response to activity / cellular response to estradiol stimulus / cellular response to amino acid stimulus / response to nicotine / protein catabolic process / response to hydrogen peroxide / metalloendopeptidase activity / cellular response to reactive oxygen species / response to estrogen / metallopeptidase activity / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / heart development / Interleukin-4 and Interleukin-13 signaling / angiogenesis / collagen-containing extracellular matrix / endopeptidase activity / Extra-nuclear estrogen signaling / response to hypoxia / positive regulation of cell migration / response to xenobiotic stimulus / serine-type endopeptidase activity / mitochondrion / proteolysis / extracellular space / zinc ion binding / extracellular region / nucleus / plasma membrane Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / Resolution: 2.15 Å | ||||||
Authors | Libson, A.M. / Gittis, A.G. / Collier, I.E. / Marmer, B.L. / Goldberg, G.G. / Lattman, E.E. | ||||||
Citation | Journal: Nat.Struct.Biol. / Year: 1995 Title: Crystal structure of the haemopexin-like C-terminal domain of gelatinase A. Authors: Libson, A.M. / Gittis, A.G. / Collier, I.E. / Marmer, B.L. / Goldberg, G.I. / Lattman, E.E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1gen.cif.gz | 60.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1gen.ent.gz | 47 KB | Display | PDB format |
PDBx/mmJSON format | 1gen.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ge/1gen ftp://data.pdbj.org/pub/pdb/validation_reports/ge/1gen | HTTPS FTP |
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-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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-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 24659.078 Da / Num. of mol.: 1 / Fragment: C-TERMINAL DOMAIN Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: HUMAN GELATINASE A / Plasmid: PFLAG1 / Gene (production host): HUMAN GELATINASE A / Production host: Escherichia coli (E. coli) / References: UniProt: P08253, gelatinase A |
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-Non-polymers , 5 types, 55 molecules
#2: Chemical | ChemComp-ZN / |
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#3: Chemical | ChemComp-CA / |
#4: Chemical | ChemComp-CL / |
#5: Chemical | ChemComp-NA / |
#6: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.42 Å3/Da / Density % sol: 40 % | |||||||||||||||||||||||||
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Crystal | *PLUS | |||||||||||||||||||||||||
Crystal grow | *PLUS pH: 6.5 / Method: vapor diffusion | |||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction source | Wavelength: 1.5418 |
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Detector | Type: RIGAKU RAXIS / Detector: IMAGE PLATE |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2→20 Å / Num. obs: 13690 / % possible obs: 92 % / Observed criterion σ(I): 1 / Redundancy: 3.5 % / Rmerge(I) obs: 0.03 |
-Processing
Software |
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Refinement | Resolution: 2.15→6.5 Å / σ(F): 4 Details: RESIDUES 529 AND 530 WERE MODELED INTO POOR ELECTRON DENSITY. THE SIDE CHAIN ORIENTATIONS WERE TAKEN FROM THE ROTAMER LIBRARY.
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Refine analyze | Luzzati coordinate error obs: 0.25 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.15→6.5 Å
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Refine LS restraints |
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Software | *PLUS Name: X-PLOR / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor Rfree: 0.26 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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