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Yorodumi- PDB-3ljz: Crystal Structure of Human MMP-13 complexed with an Amino-2-indan... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3ljz | ||||||
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Title | Crystal Structure of Human MMP-13 complexed with an Amino-2-indanol compound | ||||||
Components | Collagenase 3 | ||||||
Keywords | HYDROLASE/HYDROLASE INHIBITOR / MMP-13 inhibitor / zinc chelating agent / S1' pocket / Collagen degradation / Disease mutation / Disulfide bond / Extracellular matrix / Glycoprotein / Hydrolase / Metal-binding / Metalloprotease / Protease / Secreted / Zymogen / HYDROLASE-HYDROLASE INHIBITOR complex | ||||||
Function / homology | Function and homology information growth plate cartilage development / RUNX2 regulates genes involved in cell migration / endochondral ossification / Hydrolases; Acting on peptide bonds (peptidases); Metalloendopeptidases / bone morphogenesis / Assembly of collagen fibrils and other multimeric structures / bone mineralization / Activation of Matrix Metalloproteinases / response to amyloid-beta / Collagen degradation ...growth plate cartilage development / RUNX2 regulates genes involved in cell migration / endochondral ossification / Hydrolases; Acting on peptide bonds (peptidases); Metalloendopeptidases / bone morphogenesis / Assembly of collagen fibrils and other multimeric structures / bone mineralization / Activation of Matrix Metalloproteinases / response to amyloid-beta / Collagen degradation / collagen catabolic process / extracellular matrix disassembly / collagen binding / Degradation of the extracellular matrix / extracellular matrix / extracellular matrix organization / metalloendopeptidase activity / endopeptidase activity / serine-type endopeptidase activity / calcium ion binding / proteolysis / extracellular space / zinc ion binding / extracellular region Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2 Å | ||||||
Authors | Shieh, H.-S. / Kiefer, J.R. | ||||||
Citation | Journal: Protein Sci. / Year: 2011 Title: Structure analysis reveals the flexibility of the ADAMTS-5 active site. Authors: Shieh, H.S. / Tomasselli, A.G. / Mathis, K.J. / Schnute, M.E. / Woodard, S.S. / Caspers, N. / Williams, J.M. / Kiefer, J.R. / Munie, G. / Wittwer, A. / Malfait, A.M. / Tortorella, M.D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3ljz.cif.gz | 284.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3ljz.ent.gz | 232.8 KB | Display | PDB format |
PDBx/mmJSON format | 3ljz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3ljz_validation.pdf.gz | 1.5 MB | Display | wwPDB validaton report |
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Full document | 3ljz_full_validation.pdf.gz | 1.5 MB | Display | |
Data in XML | 3ljz_validation.xml.gz | 32.6 KB | Display | |
Data in CIF | 3ljz_validation.cif.gz | 43.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lj/3ljz ftp://data.pdbj.org/pub/pdb/validation_reports/lj/3ljz | HTTPS FTP |
-Related structure data
-Links
-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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-Components
-Protein , 1 types, 4 molecules ABCD
#1: Protein | Mass: 18418.611 Da / Num. of mol.: 4 / Fragment: UNP residues 104-267 / Mutation: Y104A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: MMP13 / Plasmid: PGEMEX1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)/PLYSS References: UniProt: P45452, Hydrolases; Acting on peptide bonds (peptidases); Metalloendopeptidases |
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-Non-polymers , 6 types, 378 molecules
#2: Chemical | ChemComp-CA / #3: Chemical | ChemComp-ZN / #4: Chemical | ChemComp-SO4 / #5: Chemical | ChemComp-LA3 / ( #6: Chemical | ChemComp-EPE / #7: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.85 Å3/Da / Density % sol: 56.91 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8 Details: Protein: 5.5 mg/ml MMP-13 with 200 uM surrogate inhibitor in 20mM Tris pH 8.5 and 5 mM CaCl2. reservoir: 1.1-1.6M Li2SO4 in 0.1M Hepes pH 7.4-8.2. drop ratio: 5ul protein + 1 ul reservoir. , ...Details: Protein: 5.5 mg/ml MMP-13 with 200 uM surrogate inhibitor in 20mM Tris pH 8.5 and 5 mM CaCl2. reservoir: 1.1-1.6M Li2SO4 in 0.1M Hepes pH 7.4-8.2. drop ratio: 5ul protein + 1 ul reservoir. , VAPOR DIFFUSION, SITTING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 110 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Mar 26, 2004 / Details: crystal monochromator |
Radiation | Monochromator: crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2→20 Å / Num. all: 53516 / Num. obs: 53516 / % possible obs: 100 % / Observed criterion σ(F): -1.5 / Observed criterion σ(I): -3 / Redundancy: 5.2 % / Biso Wilson estimate: 14.7 Å2 / Rsym value: 0.09 / Net I/σ(I): 13.8 |
Reflection shell | Resolution: 2→2.07 Å / Redundancy: 3.6 % / Mean I/σ(I) obs: 5.9 / Num. unique all: 4064 / Rsym value: 0.251 / % possible all: 71.4 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS / Resolution: 2→19.94 Å / Cor.coef. Fo:Fc: 0.922 / Cor.coef. Fo:Fc free: 0.909 / SU B: 7.232 / SU ML: 0.104 / Isotropic thermal model: TLS restrained individual / Cross valid method: THROUGHOUT / ESU R: 0.193 / ESU R Free: 0.161 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 25.406 Å2
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Refinement step | Cycle: LAST / Resolution: 2→19.94 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.001→2.052 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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