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Yorodumi- PDB-3l50: The crystal structure of human Glia Maturation Factor, Gamma (GMFG) -
+Open data
-Basic information
Entry | Database: PDB / ID: 3l50 | ||||||
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Title | The crystal structure of human Glia Maturation Factor, Gamma (GMFG) | ||||||
Components | Glia maturation factor gamma | ||||||
Keywords | HORMONE / GMFG / human / Glia Maturation Factor / Gamma / Structural Genomics / Structural Genomics Consortium / SGC / Growth factor | ||||||
Function / homology | Function and homology information : / actin filament debranching / Arp2/3 complex binding / neutrophil degranulation / negative regulation of Arp2/3 complex-mediated actin nucleation / protein kinase inhibitor activity / enzyme activator activity / growth factor activity / actin binding / secretory granule lumen ...: / actin filament debranching / Arp2/3 complex binding / neutrophil degranulation / negative regulation of Arp2/3 complex-mediated actin nucleation / protein kinase inhibitor activity / enzyme activator activity / growth factor activity / actin binding / secretory granule lumen / ficolin-1-rich granule lumen / protein phosphorylation / Neutrophil degranulation / extracellular region Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | ||||||
Authors | Ugochukwu, E. / Pilka, E. / Krysztofinska, E. / Hapka, E. / Krojer, T. / Muniz, J. / Vollmar, M. / Pike, A.C.W. / von Delft, F. / Bountra, C. ...Ugochukwu, E. / Pilka, E. / Krysztofinska, E. / Hapka, E. / Krojer, T. / Muniz, J. / Vollmar, M. / Pike, A.C.W. / von Delft, F. / Bountra, C. / Arrowsmith, C.H. / Weigelt, J. / Edwards, A. / Kavanagh, K.L. / Oppermann, U. / Structural Genomics Consortium (SGC) | ||||||
Citation | Journal: To be Published Title: The crystal structure of human Glia Maturation Factor, Gamma (GMFG) Authors: Ugochukwu, E. / Pilka, E. / Krysztofinska, E. / Hapka, E. / Krojer, T. / Muniz, J. / Vollmar, M. / Pike, A.C.W. / von Delft, F. / Kavanagh, K.L. / Oppermann, U. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3l50.cif.gz | 72 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3l50.ent.gz | 53 KB | Display | PDB format |
PDBx/mmJSON format | 3l50.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/l5/3l50 ftp://data.pdbj.org/pub/pdb/validation_reports/l5/3l50 | HTTPS FTP |
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-Related structure data
Related structure data | 1vkkS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 16104.489 Da / Num. of mol.: 2 / Fragment: ADF-H domain, residues 7-140 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: GMFG / Plasmid: pNIC28-Bsa4 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-R3-pRARE2 / References: UniProt: O60234 #2: Chemical | #3: 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: 2.19 Å3/Da / Density % sol: 43.71 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 2.0M NaCl, 10% PEG 6000, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9796 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Sep 25, 2009 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9796 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→46.21 Å / Num. obs: 22857 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5 % / Rmerge(I) obs: 0.122 / Rsym value: 0.122 / Net I/σ(I): 9.5 / Num. measured all: 114339 |
Reflection shell | Resolution: 1.9→2 Å / Redundancy: 5.1 % / Rmerge(I) obs: 0.865 / Mean I/σ(I) obs: 1.9 / Num. unique all: 16823 / Rsym value: 0.865 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1VKK Resolution: 1.9→46.21 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.911 / SU B: 9.374 / SU ML: 0.122 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.164 / ESU R Free: 0.164 / 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: BABINET MODEL WITH MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 12.504 Å2
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Refinement step | Cycle: LAST / Resolution: 1.9→46.21 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.9→1.949 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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