+Open data
-Basic information
Entry | Database: PDB / ID: 1htj | ||||||
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Title | STRUCTURE OF THE RGS-LIKE DOMAIN FROM PDZ-RHOGEF | ||||||
Components | KIAA0380 | ||||||
Keywords | SIGNALING PROTEIN / RGS-like / Regulator of G protein signaling / GEF / Guanine nucleotide exchange factor | ||||||
Function / homology | Function and homology information Sema4D induced cell migration and growth-cone collapse / regulation of small GTPase mediated signal transduction / RHOB GTPase cycle / establishment of cell polarity / NRAGE signals death through JNK / RHOC GTPase cycle / CDC42 GTPase cycle / Rho protein signal transduction / RHOA GTPase cycle / striated muscle contraction ...Sema4D induced cell migration and growth-cone collapse / regulation of small GTPase mediated signal transduction / RHOB GTPase cycle / establishment of cell polarity / NRAGE signals death through JNK / RHOC GTPase cycle / CDC42 GTPase cycle / Rho protein signal transduction / RHOA GTPase cycle / striated muscle contraction / RAC1 GTPase cycle / GTPase activator activity / guanyl-nucleotide exchange factor activity / G protein-coupled receptor binding / regulation of cell growth / G alpha (12/13) signalling events / actin cytoskeleton organization / G protein-coupled receptor signaling pathway / positive regulation of DNA-templated transcription / nucleoplasm / plasma membrane / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.2 Å | ||||||
Authors | Longenecker, K.L. / Lewis, M.E. / Chikumi, H. / Gutkind, J.S. / Derewenda, Z.S. | ||||||
Citation | Journal: Structure / Year: 2001 Title: Structure of the RGS-like domain from PDZ-RhoGEF: linking heterotrimeric g protein-coupled signaling to Rho GTPases. Authors: Longenecker, K.L. / Lewis, M.E. / Chikumi, H. / Gutkind, J.S. / Derewenda, Z.S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1htj.cif.gz | 46.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1htj.ent.gz | 36.3 KB | Display | PDB format |
PDBx/mmJSON format | 1htj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ht/1htj ftp://data.pdbj.org/pub/pdb/validation_reports/ht/1htj | 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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Details | The assymetric unit contains a protein fragment that is a single domain isolated from a multi-domain protein, and is not known to organize into multimers. |
-Components
#1: Protein | Mass: 23901.242 Da / Num. of mol.: 1 / Fragment: RGS-LIKE DOMAIN (RESIDUES 281-490) / Mutation: K463A, E465A, E466A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: KIAA0380 / Plasmid details: BASED ON PET22B / Plasmid: PHIS-PARALLEL / Production host: Escherichia coli (E. coli) / Strain (production host): B834(DE3) / References: UniProt: O15085 |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.3 Å3/Da / Density % sol: 46.82 % | |||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.8 Details: Ammonium Sulfate, PEG 400, Tris-HCl, pH 7.8, VAPOR DIFFUSION, HANGING DROP, temperature 293K | |||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 20 ℃ / pH: 8.5 / Method: vapor diffusion | |||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X9B / Wavelength: 0.9717 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Aug 1, 2000 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9717 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→20 Å / Num. all: 12161 / Num. obs: 12161 / % possible obs: 98.7 % / Redundancy: 4.8 % / Biso Wilson estimate: 38 Å2 / Rmerge(I) obs: 0.052 / Net I/σ(I): 12.1 |
Reflection shell | Resolution: 2.2→2.28 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.296 / Mean I/σ(I) obs: 4.4 / Num. unique all: 1160 / % possible all: 98.6 |
Reflection | *PLUS Lowest resolution: 20 Å / Num. measured all: 57934 |
Reflection shell | *PLUS % possible obs: 99 % |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 2.2→20 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Displacement parameters |
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.2→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.2→2.28 Å
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Software | *PLUS Name: CNS / Version: 0.9 / Classification: refinement | ||||||||||||||||||||
Refinement | *PLUS Highest resolution: 2.2 Å / Lowest resolution: 20 Å / σ(F): 0 / % reflection Rfree: 6.5 % / Rfactor all: 0.226 / Rfactor obs: 0.223 | ||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.381 / Rfactor Rwork: 0.36 |