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- PDB-1ain: CRYSTAL STRUCTURE OF HUMAN ANNEXIN I AT 2.5 ANGSTROMS RESOLUTION -

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Basic information

Entry
Database: PDB / ID: 1ain
TitleCRYSTAL STRUCTURE OF HUMAN ANNEXIN I AT 2.5 ANGSTROMS RESOLUTION
ComponentsANNEXIN I
KeywordsCALCIUM/PHOSPHOLIPID BINDING / CALCIUM-PHOSPHOLIPID BINDING complex
Function / homology
Function and homology information


regulation of interleukin-1 production / prolactin secretion / myoblast migration involved in skeletal muscle regeneration / regulation of leukocyte migration / granulocyte chemotaxis / regulation of hormone secretion / positive regulation of T-helper 1 cell differentiation / phospholipase A2 inhibitor activity / positive regulation of vesicle fusion / neutrophil clearance ...regulation of interleukin-1 production / prolactin secretion / myoblast migration involved in skeletal muscle regeneration / regulation of leukocyte migration / granulocyte chemotaxis / regulation of hormone secretion / positive regulation of T-helper 1 cell differentiation / phospholipase A2 inhibitor activity / positive regulation of vesicle fusion / neutrophil clearance / prostate gland development / negative regulation of T-helper 2 cell differentiation / positive regulation of prostaglandin biosynthetic process / endocrine pancreas development / negative regulation of interleukin-8 production / neutrophil activation / cadherin binding involved in cell-cell adhesion / peptide cross-linking / cornified envelope / positive regulation of neutrophil apoptotic process / gliogenesis / neutrophil homeostasis / hepatocyte differentiation / calcium-dependent phospholipid binding / Formyl peptide receptors bind formyl peptides and many other ligands / negative regulation of exocytosis / motile cilium / cellular response to glucocorticoid stimulus / insulin secretion / alpha-beta T cell differentiation / DNA duplex unwinding / phagocytic cup / arachidonic acid secretion / positive regulation of cell migration involved in sprouting angiogenesis / positive regulation of wound healing / G protein-coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger / monocyte chemotaxis / response to X-ray / lateral plasma membrane / Smooth Muscle Contraction / positive regulation of G1/S transition of mitotic cell cycle / cellular response to vascular endothelial growth factor stimulus / localization / phagocytosis / keratinocyte differentiation / positive regulation of T cell proliferation / positive regulation of interleukin-2 production / response to interleukin-1 / phospholipid binding / adherens junction / sarcolemma / response to peptide hormone / cellular response to hydrogen peroxide / calcium-dependent protein binding / response to estradiol / regulation of cell shape / G alpha (i) signalling events / regulation of inflammatory response / actin cytoskeleton organization / early endosome membrane / G alpha (q) signalling events / basolateral plasma membrane / collagen-containing extracellular matrix / Interleukin-4 and Interleukin-13 signaling / vesicle / adaptive immune response / cell surface receptor signaling pathway / endosome / inflammatory response / apical plasma membrane / signaling receptor binding / focal adhesion / innate immune response / lipid binding / calcium ion binding / negative regulation of apoptotic process / cell surface / signal transduction / extracellular space / extracellular exosome / extracellular region / nucleoplasm / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Annexin A1 / Annexin repeat, conserved site / Annexin repeat signature. / Annexin / Annexin / Annexin repeats / Annexin repeat / Annexin superfamily / Annexin repeat profile.
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / Resolution: 2.5 Å
AuthorsKim, S.-H.
CitationJournal: Protein Sci. / Year: 1993
Title: Crystal structure of human annexin I at 2.5 A resolution.
Authors: Weng, X. / Luecke, H. / Song, I.S. / Kang, D.S. / Kim, S.H. / Huber, R.
History
DepositionJun 3, 1992Processing site: BNL
Revision 1.0Jul 15, 1993Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ANNEXIN I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,3347
Polymers35,0931
Non-polymers2406
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)139.360, 67.500, 42.110
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein ANNEXIN I / / Coordinate model: Cα atoms only


Mass: 35093.121 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / References: UniProt: P04083
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Ca

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.82 Å3/Da / Density % sol: 56.4 %
Crystal grow
*PLUS
pH: 6.5 / Method: other
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
120 mg/mLprotein solution1drop
20.05 Mcacodylate1drop
30.1 MNa(OAc)1drop
410 mM1dropCaCl2
58 %PEG40001drop
60.1 Mcacodylate1reservoir
70.2 MNa(OAc)1reservoir
810 mM1reservoirCaCl2
916 %PEG40001reservoir

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 2.5 Å / Num. obs: 13945 / % possible obs: 97.3 % / Rmerge(I) obs: 0.0535 / Num. measured all: 76668

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Processing

Software
NameClassification
X-PLORmodel building
TNTrefinement
X-PLORphasing
RefinementRfactor Rwork: 0.163 / Highest resolution: 2.5 Å
Refinement stepCycle: LAST / Highest resolution: 2.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms314 0 6 0 320
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.017
X-RAY DIFFRACTIONx_angle_deg2.8
Refinement
*PLUS
Highest resolution: 2.5 Å / Lowest resolution: 10 Å / Rfactor obs: 0.177
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.014
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_deg2.7

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