+Open data
-Basic information
Entry | Database: PDB / ID: 1gr3 | ||||||
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Title | Structure of the human collagen X NC1 trimer | ||||||
Components | COLLAGEN X | ||||||
Keywords | COLLAGEN / EXTRACELLULAR MATRIX / CONNECTIVE TISSUE | ||||||
Function / homology | Function and homology information Collagen chain trimerization / extracellular matrix structural constituent conferring tensile strength / Collagen biosynthesis and modifying enzymes / collagen trimer / extracellular matrix structural constituent / Assembly of collagen fibrils and other multimeric structures / Collagen degradation / Non-integrin membrane-ECM interactions / Integrin cell surface interactions / extracellular matrix ...Collagen chain trimerization / extracellular matrix structural constituent conferring tensile strength / Collagen biosynthesis and modifying enzymes / collagen trimer / extracellular matrix structural constituent / Assembly of collagen fibrils and other multimeric structures / Collagen degradation / Non-integrin membrane-ECM interactions / Integrin cell surface interactions / extracellular matrix / extracellular matrix organization / skeletal system development / collagen-containing extracellular matrix / endoplasmic reticulum lumen / extracellular space / extracellular region / metal ion binding Similarity search - Function | ||||||
Biological species | HOMO SAPIENS (human) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Bogin, O. / Kvansakul, M. / Rom, E. / Singer, J. / Yayon, A. / Hohenester, E. | ||||||
Citation | Journal: Structure / Year: 2002 Title: Insight Into Schmid Metaphyseal Chondrodysplasia from the Crystal Structure of the Collagen X Nc1 Domain Trimer. Authors: Bogin, O. / Kvansakul, M. / Rom, E. / Singer, J. / Yayon, A. / Hohenester, E. #1: Journal: J.Biol.Chem. / Year: 1999 Title: Metaphyseal Chondrodysplasia Type Schmid Mutations are Predicted to Occur in Two Distinct Three-Dimensional Clusters within Type X Collagen Nc1 Domains that Retain the Ability to Trimerize Authors: Marks, D.S. / Gregory, C.A. / Wallis, G.A. / Brass, A. / Kadler, K.E. / Boot-Handford, R.P. #2: Journal: Matrix Biol. / Year: 1998 Title: Phenotypic and Biochemical Consequences of Collagen X Mutations in Mice and Humans Authors: Chan, D. / Jacenko, O. | ||||||
History |
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Remark 700 | SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1gr3.cif.gz | 45.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1gr3.ent.gz | 29.7 KB | Display | PDB format |
PDBx/mmJSON format | 1gr3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gr/1gr3 ftp://data.pdbj.org/pub/pdb/validation_reports/gr/1gr3 | HTTPS FTP |
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-Related structure data
Related structure data | 1c28S S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 17710.961 Da / Num. of mol.: 1 / Fragment: NC1 DOMAIN, RESIDUES 521-680 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: P89BLUESCRIPT / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: Q03692 | ||||||
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#2: Chemical | ChemComp-CPS / | ||||||
#3: Chemical | #4: Chemical | ChemComp-NA / | #5: Water | ChemComp-HOH / | Sequence details | N-TERMINAL FUSED 6-HIS TAG | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.24 Å3/Da / Density % sol: 45 % | |||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 6.5 / Details: 1.6 M MGSO4, 0.1 M MES PH 6.5 | |||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 9.5 / Method: vapor diffusion, hanging drop | |||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 293 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Details: OSMIC MIRRORS |
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→20 Å / Num. obs: 11537 / % possible obs: 99.9 % / Redundancy: 4.7 % / Biso Wilson estimate: 26.2 Å2 / Rmerge(I) obs: 0.076 / Net I/σ(I): 13.5 |
Reflection shell | Resolution: 2→2.1 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.385 / Mean I/σ(I) obs: 4.1 / % possible all: 100 |
Reflection | *PLUS Highest resolution: 2 Å / Lowest resolution: 20 Å |
Reflection shell | *PLUS Lowest resolution: 2.11 Å / % possible obs: 100 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1C28 Resolution: 2→20 Å / Data cutoff high absF: 10000 / Isotropic thermal model: INDIVIDUAL RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
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Solvent computation | Solvent model: FLAT / Bsol: 75 Å2 / ksol: 0.33 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.03 Å / Total num. of bins used: 23
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Xplor file |
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Software | *PLUS Name: CNS / Version: 1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 2 Å / Lowest resolution: 20 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |