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- PDB-1aii: ANNEXIN III -

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Basic information

Entry
Database: PDB / ID: 1aii
TitleANNEXIN III
ComponentsANNEXIN III
KeywordsCALCIUM/PHOSPHOLIPID BINDING PROTEIN / ANNEXIN / PHOSPHOLIPASE A2 INHIBITOR / 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 / phagocytosis / animal organ regeneration ...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 / phagocytosis / animal organ regeneration / response to glucocorticoid / positive regulation of endothelial cell migration / positive regulation of DNA-binding transcription factor activity / hippocampus development / phagocytic vesicle membrane / positive regulation of angiogenesis / calcium-dependent protein binding / defense response to bacterium / axon / neuronal cell body / dendrite / calcium ion binding / extracellular exosome / nucleus / membrane / 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
ETHANOLAMINE / Annexin A3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsLewit-Bentley, A. / Perron, B.
CitationJournal: J.Biol.Chem. / Year: 1997
Title: Can enzymatic activity, or otherwise, be inferred from structural studies of annexin III?
Authors: Perron, B. / Lewit-Bentley, A. / Geny, B. / Russo-Marie, F.
History
DepositionNov 28, 1996Processing site: BNL
Revision 1.0Mar 12, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 2, 2023Group: Database references / Derived calculations / Refinement description
Category: database_2 / pdbx_initial_refinement_model ...database_2 / pdbx_initial_refinement_model / 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_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_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_alt_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.pdbx_ptnr2_label_alt_id / _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
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection / Category: atom_site / chem_comp_atom / chem_comp_bond / Item: _atom_site.auth_atom_id / _atom_site.label_atom_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)36,7858
Polymers36,4271
Non-polymers3587
Water4,197233
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)42.290, 68.720, 50.590
Angle α, β, γ (deg.)90.00, 94.27, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein ANNEXIN III


Mass: 36427.270 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human)
Description: PLASMID SOURCE PUC (BIOGEN, CAMBRIDGE, MA, USA)
Plasmid: PGEX-2T / Production host: Escherichia coli (E. coli) / Strain (production host): NB42 / References: UniProt: P12429
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-ETA / ETHANOLAMINE


Type: L-peptide COOH carboxy terminus / Mass: 61.083 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H7NO
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 233 / Source method: isolated from a natural source / Formula: H2O

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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: 2.22 Å3/Da / Density % sol: 38.87 %
Crystal growpH: 7.8
Details: 18MG/ML PROTEIN, 10MM CACL2 IN 50 MM HEPES AT PH=7.8 WAS EQUILIBRATED AGAINST 50% AMMONIUM SULFATE IN THE SAME BUFFER.
Crystal grow
*PLUS
pH: 7.5 / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
118 mg/mlprotein1drop
210 mM1dropCaCl2
31 mM1dropMnCl2
41 mMinositol 2-phosphate1drop
525 %ammonium sulfate1drop
650 mMTris-HCl1drop
750 %ammonium sulfate1reservoir

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Data collection

DiffractionMean temperature: 300 K
Diffraction sourceSource: SYNCHROTRON / Site: LURE / Beamline: D41A / Wavelength: 1.38
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jun 8, 1995
RadiationMonochromator: GE(111) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.38 Å / Relative weight: 1
ReflectionResolution: 1.95→18.95 Å / Num. obs: 20818 / % possible obs: 98.5 % / Observed criterion σ(I): 0 / Redundancy: 2.9 % / Biso Wilson estimate: 0.6 Å2 / Rsym value: 0.072 / Net I/σ(I): 4.71
Reflection shellResolution: 1.95→2 Å / Redundancy: 2.08 % / Mean I/σ(I) obs: 4.7 / Rsym value: 0.139 / % possible all: 83.5
Reflection
*PLUS
Num. measured all: 78671 / Rmerge(I) obs: 0.072
Reflection shell
*PLUS
% possible obs: 83.5 % / Rmerge(I) obs: 0.139

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Processing

Software
NameClassification
AMoREphasing
PROLSQrefinement
MOSFLMdata reduction
CCP4data reduction
CCP4data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1AXN

1axn


Resolution: 1.95→20 Å / Cross valid method: THROUGHOUT / σ(F): 1
RfactorNum. reflection% reflectionSelection details
Rfree0.237 1039 5 %RANDOM
Rwork0.193 ---
obs0.196 20799 98.5 %-
Displacement parametersBiso mean: 18.8 Å2
Refinement stepCycle: LAST / Resolution: 1.95→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2553 0 6 233 2792
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0090.02
X-RAY DIFFRACTIONp_angle_d0.030.04
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.030.05
X-RAY DIFFRACTIONp_hb_or_metal_coord00.05
X-RAY DIFFRACTIONp_mcbond_it2.052
X-RAY DIFFRACTIONp_mcangle_it2.7042.5
X-RAY DIFFRACTIONp_scbond_it2.9292.5
X-RAY DIFFRACTIONp_scangle_it4.5473
X-RAY DIFFRACTIONp_plane_restr0.0050.02
X-RAY DIFFRACTIONp_chiral_restr0.080.12
X-RAY DIFFRACTIONp_singtor_nbd0.1770.3
X-RAY DIFFRACTIONp_multtor_nbd0.2150.3
X-RAY DIFFRACTIONp_xhyhbond_nbd0.1620.3
X-RAY DIFFRACTIONp_xyhbond_nbd0.1690.3
X-RAY DIFFRACTIONp_planar_tor1.0193
X-RAY DIFFRACTIONp_staggered_tor18.81115
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor33.51920
X-RAY DIFFRACTIONp_special_tor015
Software
*PLUS
Name: PROLSQ / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.193
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_angle_d
X-RAY DIFFRACTIONp_angle_deg2.584

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