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Yorodumi- PDB-6shr: X-RAY CRYSTAL STRUCTURE OF CELL-FREE PROTEIN SYNTHESIS (CFPS) PRO... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6shr | ||||||
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Title | X-RAY CRYSTAL STRUCTURE OF CELL-FREE PROTEIN SYNTHESIS (CFPS) PRODUCED SDF1-A | ||||||
Components | Stromal cell-derived factor 1 | ||||||
Keywords | CYTOKINE / CELL-FREE PROTEIN SYNTHESIS (CFPS) | ||||||
Function / homology | Function and homology information chemokine (C-X-C motif) ligand 12 signaling pathway / negative regulation of leukocyte tethering or rolling / response to ultrasound / telencephalon cell migration / regulation of actin polymerization or depolymerization / CXCL12-activated CXCR4 signaling pathway / chemokine receptor binding / positive regulation of vasculature development / CXCR chemokine receptor binding / positive regulation of axon extension involved in axon guidance ...chemokine (C-X-C motif) ligand 12 signaling pathway / negative regulation of leukocyte tethering or rolling / response to ultrasound / telencephalon cell migration / regulation of actin polymerization or depolymerization / CXCL12-activated CXCR4 signaling pathway / chemokine receptor binding / positive regulation of vasculature development / CXCR chemokine receptor binding / positive regulation of axon extension involved in axon guidance / positive regulation of dopamine secretion / Signaling by ROBO receptors / induction of positive chemotaxis / integrin activation / negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage / negative regulation of dendritic cell apoptotic process / cellular response to chemokine / chemokine-mediated signaling pathway / blood circulation / positive regulation of monocyte chemotaxis / Chemokine receptors bind chemokines / chemokine activity / positive regulation of calcium ion import / detection of temperature stimulus involved in sensory perception of pain / positive regulation of cell adhesion / positive regulation of T cell migration / animal organ regeneration / Nuclear signaling by ERBB4 / detection of mechanical stimulus involved in sensory perception of pain / positive regulation of neuron differentiation / positive regulation of endothelial cell proliferation / cell chemotaxis / adult locomotory behavior / axon guidance / neuron migration / response to virus / growth factor activity / defense response / intracellular calcium ion homeostasis / response to peptide hormone / chemotaxis / integrin binding / G alpha (i) signalling events / collagen-containing extracellular matrix / Estrogen-dependent gene expression / response to hypoxia / cell adhesion / immune response / G protein-coupled receptor signaling pathway / external side of plasma membrane / signaling receptor binding / signal transduction / extracellular exosome / extracellular region Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.745 Å | ||||||
Authors | Jugnarain, V.M. / Mitchell, E. / Forsyth, T. / Michael, H. / Cortes, S. / Tillier, B. | ||||||
Funding support | France, 1items
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Citation | Journal: To Be Published Title: X-RAY CRYSTAL STRUCTURE OF CELL-FREE PROTEIN SYNTHESIS (CFPS) PRODUCED SDF1-A Authors: Jugnarain, V.M. / Mitchell, E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6shr.cif.gz | 27.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6shr.ent.gz | 16.7 KB | Display | PDB format |
PDBx/mmJSON format | 6shr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/sh/6shr ftp://data.pdbj.org/pub/pdb/validation_reports/sh/6shr | HTTPS FTP |
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-Related structure data
Related structure data | 3gv3S S: Starting model for refinement |
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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: 7565.957 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CXCL12, SDF1, SDF1A, SDF1B / Production host: Escherichia coli (E. coli) / References: UniProt: P48061 |
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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: 2.72 Å3/Da / Density % sol: 54.78 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 0.1 M tri-sodium citrate pH 5.6, 20 % (v/v) isopropanol and 20 % (w/v) PEG 4000 |
-Data collection
Diffraction | Mean temperature: 293 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-1 / Wavelength: 0.966 Å |
Detector | Type: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Mar 28, 2018 |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.966 Å / Relative weight: 1 |
Reflection | Resolution: 1.74→48.49 Å / Num. obs: 9148 / % possible obs: 99.4 % / Redundancy: 7.2 % / CC1/2: 0.999 / Rmerge(I) obs: 0.062 / Rpim(I) all: 0.024 / Rrim(I) all: 0.067 / Net I/σ(I): 13.8 |
Reflection shell | Resolution: 1.74→1.77 Å / Redundancy: 7.5 % / Rmerge(I) obs: 0.968 / Num. unique obs: 842 / CC1/2: 0.668 / Rpim(I) all: 0.376 / Rrim(I) all: 1.04 / % possible all: 94.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3GV3 Resolution: 1.745→48.488 Å / Cross valid method: FREE R-VALUE
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Refinement step | Cycle: LAST / Resolution: 1.745→48.488 Å
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