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- PDB-1vkk: Crystal structure of Glia maturation factor-gamma (GMFG) from Mus... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1vkk | ||||||
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Title | Crystal structure of Glia maturation factor-gamma (GMFG) from Mus musculus at 1.50 A resolution | ||||||
![]() | Glia maturation factor gamma | ||||||
![]() | HORMONE/GROWTH FACTOR / 15079298 / GMFG / GLIA MATURATION FACTOR-GAMMA / STRUCTURAL GENOMICS / JCSG / PROTEIN STRUCTURE INITIATIVE / PSI / Joint Center for Structural Genomics / HORMONE-GROWTH FACTOR COMPLEX | ||||||
Function / homology | ![]() actin filament debranching / Arp2/3 complex binding / negative regulation of Arp2/3 complex-mediated actin nucleation / Neutrophil degranulation / growth factor activity / actin binding Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Joint Center for Structural Genomics (JCSG) | ||||||
![]() | ![]() Title: Crystal structure of Glia maturation factor-gamma (GMFG) from Mus musculus at 1.50 A resolution Authors: Joint Center for Structural Genomics (JCSG) | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 47.7 KB | Display | ![]() |
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PDB format | ![]() | 32 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 430.2 KB | Display | ![]() |
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Full document | ![]() | 430.4 KB | Display | |
Data in XML | ![]() | 9.3 KB | Display | |
Data in CIF | ![]() | 13.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1f7sS S: Starting model for refinement |
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Similar structure data | |
Other databases |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 18232.957 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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#2: Chemical | ChemComp-PO4 / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.81 Å3/Da / Density % sol: 31.56 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop, nanodrop / pH: 8.5 Details: 30% PEG-4000, 0.1M Tris hydrochloride pH 8.5,0.2M lithium sulfate monohydrate, VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC / Detector: CCD / Date: Oct 8, 2003 |
Radiation | Monochromator: Single crystal, cylindrically bent, Si(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.35→35.92 Å / Num. obs: 22189 / % possible obs: 76.6 % / Redundancy: 2.6 % / Biso Wilson estimate: 22.11 Å2 / Rsym value: 0.044 / Net I/σ(I): 16.4 |
Reflection shell | Resolution: 1.35→1.39 Å / Redundancy: 1.9 % / Mean I/σ(I) obs: 2.2 / Num. unique all: 518 / Rsym value: 0.38 / % possible all: 23.8 |
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Processing
Software |
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Refinement | Method to determine structure: ![]() Starting model: 1f7s Resolution: 1.35→35.92 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.959 / SU B: 1.954 / SU ML: 0.04 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.069 / ESU R Free: 0.074 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS 2. ARG 142 SIDE CHAIN CONFORMATION IS SUSPICIOUS. ITS DENSITY IS POOR. 3. THE NOMINAL RESOLUTION IS 1.50 A WITH 2779 OBSERVED REFLECTIONS ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS 2. ARG 142 SIDE CHAIN CONFORMATION IS SUSPICIOUS. ITS DENSITY IS POOR. 3. THE NOMINAL RESOLUTION IS 1.50 A WITH 2779 OBSERVED REFLECTIONS BETWEEN 1.50-1.35A (35% COMPLETE FOR THIS SHELL) INCLUDED IN THE REFINEMENT. 4. TEMPERATURE FACTORS WERE REFINED AS ISOTROPIC
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 14.682 Å2
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Refinement step | Cycle: LAST / Resolution: 1.35→35.92 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.35→1.385 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Origin x: -0.052 Å / Origin y: 1.213 Å / Origin z: -1.971 Å
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Refinement TLS group | Selection: ALL |