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Yorodumi- PDB-2l0p: Solution structure of human apo-S100A1 protein by NMR spectroscopy -
+Open data
-Basic information
Entry | Database: PDB / ID: 2l0p | ||||||
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Title | Solution structure of human apo-S100A1 protein by NMR spectroscopy | ||||||
Components | S100 calcium binding protein A1 | ||||||
Keywords | Calcium binding protein / S100A1 / EF-hand / S100 family | ||||||
Function / homology | Function and homology information Regulation of TLR by endogenous ligand / MyD88 deficiency (TLR2/4) / S100 protein binding / regulation of heart contraction / IRAK4 deficiency (TLR2/4) / MyD88:MAL(TIRAP) cascade initiated on plasma membrane / positive regulation of sprouting angiogenesis / substantia nigra development / sarcoplasmic reticulum / positive regulation of nitric-oxide synthase activity ...Regulation of TLR by endogenous ligand / MyD88 deficiency (TLR2/4) / S100 protein binding / regulation of heart contraction / IRAK4 deficiency (TLR2/4) / MyD88:MAL(TIRAP) cascade initiated on plasma membrane / positive regulation of sprouting angiogenesis / substantia nigra development / sarcoplasmic reticulum / positive regulation of nitric-oxide synthase activity / calcium-dependent protein binding / ATPase binding / ER-Phagosome pathway / intracellular signal transduction / calcium ion binding / Golgi apparatus / protein homodimerization activity / protein-containing complex / mitochondrion / extracellular region / nucleoplasm / identical protein binding / nucleus / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | SOLUTION NMR / simulated annealing | ||||||
Authors | Nowakowski, M. / Jaremko, L. / Jaremko, M. / Bierzynski, A. / Zhukov, I. / Ejchart, A. | ||||||
Citation | Journal: J.Struct.Biol. / Year: 2011 Title: Solution NMR structure and dynamics of human apo-S100A1 protein. Authors: Nowakowski, M. / Jaremko, L. / Jaremko, M. / Zhukov, I. / Belczyk, A. / Bierzynski, A. / Ejchart, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2l0p.cif.gz | 1.1 MB | Display | PDBx/mmCIF format |
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PDB format | pdb2l0p.ent.gz | 928.9 KB | Display | PDB format |
PDBx/mmJSON format | 2l0p.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/l0/2l0p ftp://data.pdbj.org/pub/pdb/validation_reports/l0/2l0p | HTTPS FTP |
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-Related structure data
Similar structure data | |
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Other databases |
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-Links
-Assembly
Deposited unit |
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1 |
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NMR ensembles |
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-Components
#1: Protein | Mass: 10556.783 Da / Num. of mol.: 2 / Fragment: UNP residues 54-147 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: S100A1, RP1-178F15.1-003, hCG_15470 / Production host: Escherichia coli (E. coli) / References: UniProt: Q5T7Y6, UniProt: P23297*PLUS |
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-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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NMR experiment |
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-Sample preparation
Details |
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Sample |
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Sample conditions | pH: 6.8 / Temperature: 310 K |
-NMR measurement
NMR spectrometer |
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-Processing
NMR software |
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Refinement | Method: simulated annealing / Software ordinal: 1 / Details: standrad sa.inp xplor protocol | ||||||||||||||||||||||||
NMR constraints | NOE constraints total: 3184 / NOE intraresidue total count: 566 / NOE long range total count: 544 / NOE medium range total count: 868 / NOE sequential total count: 942 / Hydrogen bond constraints total count: 186 / Protein chi angle constraints total count: 0 / Protein other angle constraints total count: 0 / Protein phi angle constraints total count: 63 / Protein psi angle constraints total count: 63 | ||||||||||||||||||||||||
NMR representative | Selection criteria: lowest energy | ||||||||||||||||||||||||
NMR ensemble | Conformer selection criteria: structures with the lowest energy Conformers calculated total number: 130 / Conformers submitted total number: 20 / Maximum lower distance constraint violation: 0 Å / Maximum upper distance constraint violation: 0 Å / Torsion angle constraint violation method: xplor NIH | ||||||||||||||||||||||||
NMR ensemble rms | Distance rms dev: 0.0055 Å / Distance rms dev error: 0.0003 Å |