+Open data
-Basic information
Entry | Database: PDB / ID: 1agq | ||||||
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Title | GLIAL CELL-DERIVED NEUROTROPHIC FACTOR FROM RAT | ||||||
Components | GLIAL CELL-DERIVED NEUROTROPHIC FACTOR | ||||||
Keywords | GROWTH FACTOR / NEUROTROPHIC FACTOR / CYSTINE KNOT | ||||||
Function / homology | Function and homology information regulation of ureteric bud formation / mesenchymal to epithelial transition involved in metanephros morphogenesis / dorsal spinal cord development / postsynaptic membrane organization / positive regulation of mesenchymal to epithelial transition involved in metanephros morphogenesis / ureteric bud formation / positive regulation of ureteric bud formation / regulation of semaphorin-plexin signaling pathway / postganglionic parasympathetic fiber development / positive regulation of monooxygenase activity ...regulation of ureteric bud formation / mesenchymal to epithelial transition involved in metanephros morphogenesis / dorsal spinal cord development / postsynaptic membrane organization / positive regulation of mesenchymal to epithelial transition involved in metanephros morphogenesis / ureteric bud formation / positive regulation of ureteric bud formation / regulation of semaphorin-plexin signaling pathway / postganglionic parasympathetic fiber development / positive regulation of monooxygenase activity / glial cell-derived neurotrophic factor receptor binding / RET signaling / regulation of morphogenesis of a branching structure / regulation of dopamine uptake involved in synaptic transmission / enteric nervous system development / peristalsis / positive regulation of branching involved in ureteric bud morphogenesis / peripheral nervous system development / sympathetic nervous system development / organ induction / commissural neuron axon guidance / metanephros development / mRNA stabilization / RAF/MAP kinase cascade / neural crest cell migration / ureteric bud development / branching involved in ureteric bud morphogenesis / midbrain development / negative regulation of extrinsic apoptotic signaling pathway in absence of ligand / embryonic organ development / cellular response to dexamethasone stimulus / positive regulation of cell differentiation / growth factor activity / neuron differentiation / receptor tyrosine kinase binding / response to wounding / male gonad development / positive regulation of peptidyl-tyrosine phosphorylation / neuron projection development / retina development in camera-type eye / nervous system development / regulation of gene expression / negative regulation of neuron apoptotic process / cell population proliferation / receptor complex / receptor ligand activity / positive regulation of cell population proliferation / Golgi apparatus / protein homodimerization activity / positive regulation of transcription by RNA polymerase II / extracellular space / extracellular region Similarity search - Function | ||||||
Biological species | Rattus norvegicus (Norway rat) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 1.9 Å | ||||||
Authors | Eigenbrot, C. / Gerber, N. | ||||||
Citation | Journal: Nat.Struct.Biol. / Year: 1997 Title: X-ray structure of glial cell-derived neurotrophic factor at 1.9 A resolution and implications for receptor binding. Authors: Eigenbrot, C. / Gerber, N. #1: Journal: Annu.Rev.Biophys.Biomol.Struct. / Year: 1995 Title: The Cystine-Knot Growth-Factor Superfamily Authors: Sun, P.D. / Davies, D.R. #2: Journal: Science / Year: 1993 Title: A Glial Cell Line-Derived Neurotrophic Factor for Midbrain Dopaminergic Neurons Authors: Lin, L.F. / Doherty, D.H. / Lile, J.D. / Bektesh, S. / Collins, F. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1agq.cif.gz | 89 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1agq.ent.gz | 72.4 KB | Display | PDB format |
PDBx/mmJSON format | 1agq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1agq_validation.pdf.gz | 387.8 KB | Display | wwPDB validaton report |
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Full document | 1agq_full_validation.pdf.gz | 394.1 KB | Display | |
Data in XML | 1agq_validation.xml.gz | 8.9 KB | Display | |
Data in CIF | 1agq_validation.cif.gz | 15.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ag/1agq ftp://data.pdbj.org/pub/pdb/validation_reports/ag/1agq | HTTPS FTP |
-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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Noncrystallographic symmetry (NCS) | NCS oper:
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-Components
#1: Protein | Mass: 15090.256 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rattus norvegicus (Norway rat) / Cell: GLIA / Organ: BRAIN / Production host: Escherichia coli (E. coli) / References: UniProt: Q07731 #2: 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: 2.4 Å3/Da / Density % sol: 42 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 7 / Details: 20% PEG 6000, 0.8 M LICL, PH 7.0 | ||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||||||||
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: CHESS / Beamline: F1 / Wavelength: 0.918 |
Detector | Type: PRINCETON 2K / Detector: CCD / Date: Feb 1, 1996 / Details: MIRRORS |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.918 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→20 Å / Num. obs: 46219 / % possible obs: 99.6 % / Observed criterion σ(I): 0 / Redundancy: 6.5 % / Biso Wilson estimate: 22.8 Å2 / Rmerge(I) obs: 0.038 / Rsym value: 0.054 / Net I/σ(I): 14.9 |
Reflection shell | Resolution: 1.9→1.97 Å / Redundancy: 2.4 % / Mean I/σ(I) obs: 5 / Rsym value: 0.228 / % possible all: 98.1 |
-Processing
Software |
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Refinement | Method to determine structure: MIR / Resolution: 1.9→20 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 100000 / Data cutoff low absF: 0.1 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 Details: RESOLUTION-DEPENDENT WEIGHTING SCHEME USED. BULK SOLVENT MODEL USED. THERE ARE 139 ATOMS ASSIGNED ZERO OCCUPANCY. SOME OF THESE WERE USED WITH UNIT OCCUPANCY AT SOME STAGE OF REFINEMENT, BUT ...Details: RESOLUTION-DEPENDENT WEIGHTING SCHEME USED. BULK SOLVENT MODEL USED. THERE ARE 139 ATOMS ASSIGNED ZERO OCCUPANCY. SOME OF THESE WERE USED WITH UNIT OCCUPANCY AT SOME STAGE OF REFINEMENT, BUT ARE NOW ASSIGNED ZERO OCCUPANCY. THE SEGMENT C 116 - C 120 IS POORLY MODELED USING A SINGLE MAIN CHAIN CONFORMATION. THERE IS RESIDUAL ELECTRON DENSITY SUGGESTING ADDITIONAL CONFORMATION(S), BUT NO ATTEMPT TO MODEL THEM HAS BEEN MADE. ALL RESIDUE NUMBERS IN THIS ENTRY ARE GREATER (BY ONE) THAN THOSE USED IN THE JOURNAL ARTICLE DESCRIBING THIS WORK (JRNL RECORD).
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Displacement parameters | Biso mean: 33.8 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.9→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.9→1.97 Å / Rfactor Rfree error: 0.014 / Total num. of bins used: 10
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Xplor file |
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Software | *PLUS Name: X-PLOR / Version: 3.851 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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