+Open data
-Basic information
Entry | Database: PDB / ID: 1iap | ||||||
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Title | CRYSTAL STRUCTURE OF P115RHOGEF RGRGS DOMAIN | ||||||
Components | GUANINE NUCLEOTIDE EXCHANGE FACTOR P115RHOGEF | ||||||
Keywords | SIGNALING PROTEIN / p115 / RhoGEF / RGS / RGRGS | ||||||
Function / homology | Function and homology information regulation of small GTPase mediated signal transduction / RHOB GTPase cycle / NRAGE signals death through JNK / RHOC GTPase cycle / Rho protein signal transduction / RHOA GTPase cycle / GTPase activator activity / guanyl-nucleotide exchange factor activity / G protein-coupled receptor binding / G alpha (12/13) signalling events ...regulation of small GTPase mediated signal transduction / RHOB GTPase cycle / NRAGE signals death through JNK / RHOC GTPase cycle / Rho protein signal transduction / RHOA GTPase cycle / GTPase activator activity / guanyl-nucleotide exchange factor activity / G protein-coupled receptor binding / G alpha (12/13) signalling events / G protein-coupled receptor signaling pathway / RNA binding / plasma membrane / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | ||||||
Authors | Sprang, S.R. / Chen, Z. | ||||||
Citation | Journal: Nat.Struct.Biol. / Year: 2001 Title: Structure of the rgRGS domain of p115RhoGEF. Authors: Chen, Z. / Wells, C.D. / Sternweis, P.C. / Sprang, S.R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1iap.cif.gz | 51.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1iap.ent.gz | 37.1 KB | Display | PDB format |
PDBx/mmJSON format | 1iap.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ia/1iap ftp://data.pdbj.org/pub/pdb/validation_reports/ia/1iap | HTTPS FTP |
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-Related structure data
Related structure data | |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 24276.924 Da / Num. of mol.: 1 / Fragment: N-TERMINAL RGS DOMAIN Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Plasmid: PTRCC / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: Q92888 |
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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: 1.73 Å3/Da / Density % sol: 28.3 % | ||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 9.5 Details: PEG 3350, ammonium formate, CHES, pH 9.5, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K | ||||||||||||||||||||
Crystal grow | *PLUS Temperature: 20 ℃ / Method: vapor diffusion / PH range low: 9.6 / PH range high: 9.3 | ||||||||||||||||||||
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: ALS / Beamline: 5.0.2 / Wavelength: 0.976 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Jan 1, 2001 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.976 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→16 Å / Num. all: 14781 / Num. obs: 13303 / % possible obs: 90 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.8 % / Biso Wilson estimate: 18.6 Å2 / Rmerge(I) obs: 0.12 / Rsym value: 0.12 / Net I/σ(I): 12.1 |
Reflection shell | Resolution: 1.9→1.97 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.485 / Mean I/σ(I) obs: 4.8 / Num. unique all: 1152 / Rsym value: 0.485 / % possible all: 79.6 |
Reflection shell | *PLUS % possible obs: 79.6 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: SE-MET STRUCTURE OF THE SAME PROTEIN SOLVED BY MAD PHASING FROM A FOUR-WAVELENGTH MAD DATASET COLLECTED AT CHESS F2 BEAMLINE (UNPUBLISHED DATA) Resolution: 1.9→15.55 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 1423020.44 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 48.57 Å2 / ksol: 0.364 e/Å3 | |||||||||||||||||||||||||
Displacement parameters | Biso mean: 33 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.9→15.55 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.9→2.02 Å / Rfactor Rfree error: 0.025 / Total num. of bins used: 6
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Xplor file |
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Software | *PLUS Name: CNS / Version: 0.9 / Classification: refinement | |||||||||||||||||||||||||
Refinement | *PLUS σ(F): 0 / % reflection Rfree: 10.3 % | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 33 Å2 | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.339 / % reflection Rfree: 9.4 % / Rfactor Rwork: 0.304 |