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- PDB-1mcx: STRUCTURE OF FULL-LENGTH ANNEXIN A1 IN THE PRESENCE OF CALCIUM -

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Basic information

Entry
Database: PDB / ID: 1mcx
TitleSTRUCTURE OF FULL-LENGTH ANNEXIN A1 IN THE PRESENCE OF CALCIUM
ComponentsANNEXIN I
KeywordsMETAL BINDING PROTEIN / calcium/phospholipid binding protein
Function / homology
Function and homology information


regulation of interleukin-1 production / granulocyte chemotaxis / regulation of leukocyte migration / positive regulation of T-helper 1 cell differentiation / phospholipase A2 inhibitor activity / regulation of hormone secretion / neutrophil activation / calcium-dependent phospholipid binding / negative regulation of T-helper 2 cell differentiation / vesicle membrane ...regulation of interleukin-1 production / granulocyte chemotaxis / regulation of leukocyte migration / positive regulation of T-helper 1 cell differentiation / phospholipase A2 inhibitor activity / regulation of hormone secretion / neutrophil activation / calcium-dependent phospholipid binding / negative regulation of T-helper 2 cell differentiation / vesicle membrane / negative regulation of exocytosis / motile cilium / cellular response to glucocorticoid stimulus / positive regulation of wound healing / phosphatidylserine binding / monocyte chemotaxis / lateral plasma membrane / G protein-coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger / phagocytosis / phagocytic cup / positive regulation of T cell proliferation / positive regulation of interleukin-2 production / regulation of cell shape / regulation of inflammatory response / actin cytoskeleton organization / early endosome membrane / basolateral plasma membrane / adaptive immune response / apical plasma membrane / inflammatory response / innate immune response / calcium ion binding / signal transduction / extracellular space / extracellular exosome / nucleus / plasma membrane / cytoplasm
Similarity search - Function
Annexin A1 / Annexin / Annexin repeat, conserved site / Annexin repeat signature. / Annexin / Annexin / Annexin repeats / Annexin repeat / Annexin superfamily / Annexin repeat profile. ...Annexin A1 / Annexin / Annexin repeat, conserved site / Annexin repeat signature. / Annexin / Annexin / Annexin repeats / Annexin repeat / Annexin superfamily / Annexin repeat profile. / Annexin V; domain 1 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesSus scrofa (pig)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.03 Å
AuthorsLuecke, H. / Rosengarth, A.
CitationJournal: J.Mol.Biol. / Year: 2003
Title: A Calcium-driven Conformational Switch of the N-terminaland Core Domains of Annexin A1
Authors: Luecke, H. / Rosengarth, A.
History
DepositionAug 6, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 4, 2003Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 27, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 13, 2024Group: Data collection / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_initial_refinement_model / pdbx_modification_feature

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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)39,1239
Polymers38,8021
Non-polymers3218
Water6,954386
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)129.483, 129.483, 66.676
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein ANNEXIN I / Lipocortin I / Calpactin II / Chromobindin 9 / P35 / Phospholipase A2 inhibitory protein


Mass: 38802.355 Da / Num. of mol.: 1 / Mutation: S51L, H69L, L231P, N289I
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sus scrofa (pig) / Gene: ANXA1 / Plasmid: pKK233-3, pKKanx1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: P19619
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 386 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.6 Å3/Da / Density % sol: 65.84 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8
Details: PEG 1000, imidazol, calciumacetate, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal grow
*PLUS
Method: unknown
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
110 %(w/v)PEG100011
250 mMimidazole11pH8.0
3100 mMcadmium acetate11

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 26, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.03→60 Å / Num. obs: 37069 / Observed criterion σ(I): -3 / Redundancy: 15.3 % / Rmerge(I) obs: 0.117 / Net I/σ(I): 27.2
Reflection
*PLUS
Lowest resolution: 60 Å / % possible obs: 97.9 % / Num. measured all: 568454
Reflection shell
*PLUS
Highest resolution: 2.03 Å / Lowest resolution: 2.07 Å / % possible obs: 95.7 % / Rmerge(I) obs: 0.891 / Mean I/σ(I) obs: 3.3

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1HM6

1hm6


Resolution: 2.03→60 Å / Isotropic thermal model: isotropic / Cross valid method: Rfree / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.231 3325 -random
Rwork0.196 ---
all-37069 --
obs-33439 8 %-
Displacement parametersBiso mean: 26.7 Å2
Refinement stepCycle: LAST / Resolution: 2.03→60 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2394 0 8 386 2788
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.06
X-RAY DIFFRACTIONc_bond_d0.005
Refinement
*PLUS
Lowest resolution: 60 Å / Rfactor Rfree: 0.2311 / Rfactor Rwork: 0.1962
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: c_angle_deg / Dev ideal: 1.061

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