+Open data
-Basic information
Entry | Database: PDB / ID: 1lxi | ||||||
---|---|---|---|---|---|---|---|
Title | Refinement of BMP7 crystal structure | ||||||
Components | BONE MORPHOGENETIC PROTEIN 7 | ||||||
Keywords | HORMONE/GROWTH FACTOR / Cystine-knot growth factor / HORMONE-GROWTH FACTOR COMPLEX | ||||||
Function / homology | Function and homology information negative regulation of prostatic bud formation / negative regulation of mesenchymal cell apoptotic process involved in nephron morphogenesis / negative regulation of glomerular mesangial cell proliferation / mesenchymal cell apoptotic process involved in nephron morphogenesis / positive regulation of cardiac neural crest cell migration involved in outflow tract morphogenesis / positive regulation of hyaluranon cable assembly / chorio-allantoic fusion / metanephric mesenchyme morphogenesis / nephrogenic mesenchyme morphogenesis / negative regulation of striated muscle cell apoptotic process ...negative regulation of prostatic bud formation / negative regulation of mesenchymal cell apoptotic process involved in nephron morphogenesis / negative regulation of glomerular mesangial cell proliferation / mesenchymal cell apoptotic process involved in nephron morphogenesis / positive regulation of cardiac neural crest cell migration involved in outflow tract morphogenesis / positive regulation of hyaluranon cable assembly / chorio-allantoic fusion / metanephric mesenchyme morphogenesis / nephrogenic mesenchyme morphogenesis / negative regulation of striated muscle cell apoptotic process / embryonic skeletal joint morphogenesis / neural fold elevation formation / ameloblast differentiation / positive regulation of epithelial cell differentiation / metanephric mesenchymal cell proliferation involved in metanephros development / embryonic camera-type eye morphogenesis / mesenchyme development / monocyte aggregation / allantois development / mesonephros development / regulation of removal of superoxide radicals / hindbrain development / mesenchymal cell differentiation / BMP receptor binding / pericardium morphogenesis / endocardial cushion formation / pharyngeal system development / heart trabecula morphogenesis / cellular response to BMP stimulus / embryonic pattern specification / branching involved in salivary gland morphogenesis / regulation of phosphorylation / response to vitamin D / metanephros development / negative regulation of mitotic nuclear division / cardiac muscle tissue development / negative regulation of non-canonical NF-kappaB signal transduction / positive regulation of heterotypic cell-cell adhesion / cartilage development / positive regulation of dendrite development / embryonic limb morphogenesis / Molecules associated with elastic fibres / ureteric bud development / negative regulation of NF-kappaB transcription factor activity / regulation of branching involved in prostate gland morphogenesis / branching morphogenesis of an epithelial tube / negative regulation of Notch signaling pathway / cardiac septum morphogenesis / dendrite development / odontogenesis of dentin-containing tooth / positive regulation of SMAD protein signal transduction / mesoderm formation / negative regulation of cell cycle / negative regulation of neuron differentiation / epithelial to mesenchymal transition / BMP signaling pathway / positive regulation of osteoblast differentiation / positive regulation of bone mineralization / positive regulation of epithelial to mesenchymal transition / Transcriptional regulation of brown and beige adipocyte differentiation by EBF2 / positive regulation of brown fat cell differentiation / positive regulation of neuron differentiation / ossification / neuron projection morphogenesis / skeletal system development / cytokine activity / axon guidance / growth factor activity / response to peptide hormone / negative regulation of neurogenesis / response to estradiol / heparin binding / cellular response to hypoxia / collagen-containing extracellular matrix / vesicle / positive regulation of apoptotic process / negative regulation of DNA-templated transcription / positive regulation of gene expression / positive regulation of DNA-templated transcription / positive regulation of transcription by RNA polymerase II / extracellular space / extracellular region Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Greenwald, J. / Groppe, J. / Kwiatkowski, W. / Choe, S. | ||||||
Citation | Journal: Mol.Cell / Year: 2003 Title: The BMP7/ActRII Extracellular Domain Complex Provides New Insights into the Cooperative Nature of Receptor Assembly Authors: Greenwald, J. / Groppe, J. / Gray, P. / Wiater, E. / Kwiatkowski, W. / Vale, W. / Choe, S. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1lxi.cif.gz | 33 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1lxi.ent.gz | 25.2 KB | Display | PDB format |
PDBx/mmJSON format | 1lxi.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lx/1lxi ftp://data.pdbj.org/pub/pdb/validation_reports/lx/1lxi | HTTPS FTP |
---|
-Related structure data
Related structure data | 1lx5C 1bmpS S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
| ||||||||
Details | The second part of the biological assembly is generated by the two fold axis: x-y+1,-y+2,1/3-z |
-Components
#1: Protein | Mass: 15699.730 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Description: DHFR- / Gene: BMP7 / Cell (production host): OVARY CELLS / Production host: Cricetulus griseus (Chinese hamster) / References: UniProt: P18075 |
---|---|
#2: Sugar | ChemComp-NAG / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 3.94 Å3/Da / Density % sol: 68.8 % | ||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 4.5 Details: 20% MPD, 0.1M Sodium Acetate, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K | ||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 23 ℃ | ||||||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL9-1 / Wavelength: 0.98 Å |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Sep 1, 2000 / Details: mirror |
Radiation | Monochromator: Si 311 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 2→25 Å / Num. all: 15770 / Num. obs: 15770 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Rsym value: 0.054 / Net I/σ(I): 16.9 |
Reflection shell | Resolution: 2→2.08 Å / Rsym value: 0.333 / % possible all: 99.6 |
Reflection | *PLUS Highest resolution: 2 Å / Lowest resolution: 100 Å / % possible obs: 93.3 % / Num. measured all: 67831 / Rmerge(I) obs: 0.054 |
Reflection shell | *PLUS Highest resolution: 2 Å / % possible obs: 99.6 % / Rmerge(I) obs: 0.333 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 1BMP Resolution: 2→23.96 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.934 / SU B: 4.128 / SU ML: 0.119 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.137 / ESU R Free: 0.127 / Stereochemistry target values: Engh & Huber / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 35.983 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→23.96 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2→2.052 Å / Total num. of bins used: 20 /
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Software | *PLUS Version: 5 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 2 Å / Lowest resolution: 40 Å / % reflection Rfree: 5 % / Rfactor Rfree: 0.244 / Rfactor Rwork: 0.228 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
|