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- PDB-1axn: THE HIGH RESOLUTION STRUCTURE OF ANNEXIN III SHOWS DIFFERENCES WI... -

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Basic information

Entry
Database: PDB / ID: 1axn
TitleTHE HIGH RESOLUTION STRUCTURE OF ANNEXIN III SHOWS DIFFERENCES WITH ANNEXIN V
ComponentsANNEXIN III
KeywordsCALCIUM/PHOSPHOLIPID-BINDING PROTEIN / ANNEXIN FAMILY / CALCIUM-PHOSPHOLIPID-BINDING PROTEIN COMPLEX
Function / homology
Function and homology information


neutrophil degranulation / phospholipase A2 inhibitor activity / positive regulation of DNA metabolic process / specific granule / response to growth factor / calcium-dependent phospholipid binding / vesicle membrane / phosphatidylserine binding / animal organ regeneration / phagocytosis ...neutrophil degranulation / phospholipase A2 inhibitor activity / positive regulation of DNA metabolic process / specific granule / response to growth factor / calcium-dependent phospholipid binding / vesicle membrane / phosphatidylserine binding / animal organ regeneration / phagocytosis / response to glucocorticoid / positive regulation of endothelial cell migration / hippocampus development / positive regulation of DNA-binding transcription factor activity / positive regulation of angiogenesis / phagocytic vesicle membrane / calcium-dependent protein binding / defense response to bacterium / axon / neuronal cell body / dendrite / calcium ion binding / extracellular exosome / membrane / nucleus / plasma membrane / cytoplasm
Similarity search - Function
Annexin A3 / Annexin / Annexin repeat, conserved site / Annexin repeat signature. / Annexin / Annexin / Annexin repeats / Annexin repeat / Annexin superfamily / Annexin repeat profile. ...Annexin A3 / 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 speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.78 Å
AuthorsFavier-Perron, B. / Lewit-Bentley, A. / Russo-Marie, F.
CitationJournal: Biochemistry / Year: 1996
Title: The high-resolution crystal structure of human annexin III shows subtle differences with annexin V.
Authors: Favier-Perron, B. / Lewit-Bentley, A. / Russo-Marie, F.
History
DepositionAug 21, 1995Processing site: BNL
Revision 1.0Mar 8, 1996Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _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.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _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.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.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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ANNEXIN III
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,5846
Polymers36,3831
Non-polymers2005
Water5,062281
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)42.544, 69.085, 50.950
Angle α, β, γ (deg.)90.00, 95.55, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein ANNEXIN III


Mass: 36383.148 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: HUMAN RECOMBINANT / Source: (gene. exp.) Homo sapiens (human) / Description: PREPARED AS A GST-FUSION, THEN CLEAVED YES / Gene: HUMAN ANNEXIN III / Plasmid: PGEX2T / Gene (production host): HUMAN ANNEXIN III / Production host: Escherichia coli (E. coli) / References: UniProt: P12429
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 281 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.05 Å3/Da / Density % sol: 39.94 %
Crystal
*PLUS
Density % sol: 42 %
Crystal grow
*PLUS
pH: 7.5 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
118 mg/mlprotein1drop
210 mM1dropCaCl2
325 %ammonium sulfate1drop
450 mMTris-HCl1drop
550 %ammonium sulfate1reservoir

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: LURE / Beamline: DW32 / Wavelength: 0.9
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Apr 13, 1994
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.78→100 Å / Num. obs: 25718 / % possible obs: 92 % / Observed criterion σ(I): 0 / Redundancy: 3.45 % / Rmerge(I) obs: 0.043
Reflection
*PLUS
Lowest resolution: 23.8 Å / Num. measured all: 88603 / Rmerge(I) obs: 0.043
Reflection shell
*PLUS
Highest resolution: 1.78 Å / Lowest resolution: 1.83 Å / % possible obs: 79.2 %

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Processing

Software
NameClassification
PROLSQrefinement
MARXDSdata reduction
RefinementResolution: 1.78→8 Å / σ(F): 2 /
RfactorNum. reflection
Rfree0.221 -
obs0.177 25485
Displacement parametersBiso mean: 20.2 Å2
Refinement stepCycle: LAST / Resolution: 1.78→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2560 0 5 281 2846
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.010.02
X-RAY DIFFRACTIONp_angle_d0.0320.04
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0320.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it1.351.5
X-RAY DIFFRACTIONp_mcangle_it2.152
X-RAY DIFFRACTIONp_scbond_it2.5822
X-RAY DIFFRACTIONp_scangle_it4.0382.5
X-RAY DIFFRACTIONp_plane_restr0.0150.006
X-RAY DIFFRACTIONp_chiral_restr0.120.085
X-RAY DIFFRACTIONp_singtor_nbd0.1890.3
X-RAY DIFFRACTIONp_multtor_nbd0.1990.3
X-RAY DIFFRACTIONp_xhyhbond_nbd0.1870.3
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor11.068
X-RAY DIFFRACTIONp_staggered_tor19.419.431
X-RAY DIFFRACTIONp_orthonormal_tor31.731.794
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor
Software
*PLUS
Name: PROLSQ / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.173 / Rfactor Rfree: 0.242
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.009
X-RAY DIFFRACTIONp_angle_d
X-RAY DIFFRACTIONp_planar_d
X-RAY DIFFRACTIONp_plane_restr0.088
X-RAY DIFFRACTIONp_chiral_restr1.201
X-RAY DIFFRACTIONp_mcbond_it
X-RAY DIFFRACTIONp_scbond_it
X-RAY DIFFRACTIONp_mcangle_it
X-RAY DIFFRACTIONp_scangle_it

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