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- PDB-1ala: STRUCTURE OF CHICKEN ANNEXIN V AT 2.25-ANGSTROMS RESOLUTION -

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Basic information

Entry
Database: PDB / ID: 1ala
TitleSTRUCTURE OF CHICKEN ANNEXIN V AT 2.25-ANGSTROMS RESOLUTION
ComponentsANNEXIN V
KeywordsCALCIUM/PHOSPHOLIPID-BINDING PROTEIN / CALCIUM-PHOSPHOLIPID-BINDING PROTEIN complex
Function / homology
Function and homology information


Platelet degranulation / negative regulation of coagulation / calcium-dependent phospholipid binding / vesicle membrane / phosphatidylserine binding / calcium ion homeostasis / calcium channel complex / sarcolemma / calcium channel activity / vesicle ...Platelet degranulation / negative regulation of coagulation / calcium-dependent phospholipid binding / vesicle membrane / phosphatidylserine binding / calcium ion homeostasis / calcium channel complex / sarcolemma / calcium channel activity / vesicle / calcium ion binding / cytoplasm
Similarity search - Function
Annexin A5 / Annexin / Annexin repeat, conserved site / Annexin repeat signature. / Annexin / Annexin / Annexin repeats / Annexin repeat / Annexin superfamily / Annexin repeat profile. ...Annexin A5 / 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 speciesGallus gallus (chicken)
MethodX-RAY DIFFRACTION / Resolution: 2.25 Å
AuthorsWaller, D.A. / Bewley, M.C. / Huber, R.
Citation
Journal: Biochemistry / Year: 1993
Title: Structure of chicken annexin V at 2.25-A resolution.
Authors: Bewley, M.C. / Boustead, C.M. / Walker, J.H. / Waller, D.A. / Huber, R.
#1: Journal: Biochem.Soc.Trans. / Year: 1992
Title: Annexin V, a Calcium-Dependent Phospholipid-Binding Protein
Authors: Walker, J.H. / Boustead, C.M. / Koster, J.J. / Bewley, M. / Waller, D.A.
#2: Journal: FEBS Lett. / Year: 1991
Title: Crystallization and Preliminary X-Ray Studies of Annexin Iv (Endonexin), a Calcium-Dependent Phospholipid-Binding Protein
Authors: Boustead, C.M. / Walker, J.H. / Kennedy, D. / Waller, D.A.
History
DepositionJan 14, 1993Processing site: BNL
Revision 1.0Oct 31, 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 ...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_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_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.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_ref_seq_dif.details / _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

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Assembly

Deposited unit
A: ANNEXIN V
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,3834
Polymers36,2621
Non-polymers1203
Water1,45981
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)99.400, 99.400, 96.200
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3
Atom site foot note1: RESIDUE 14 IS A CIS PROLINE.

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Components

#1: Protein ANNEXIN V


Mass: 36262.355 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gallus gallus (chicken) / References: UniProt: P17153
#2: Chemical ChemComp-CA / CALCIUM ION


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


Mass: 18.015 Da / Num. of mol.: 81 / 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: 2.52 Å3/Da / Density % sol: 51.23 %
Crystal grow
*PLUS
Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
110 mg/mLprotein solution1drop
220 mMTris-HCl1drop
32.1 Mammonium sulfate1reservoir
420 mMTris-HCl1reservoir
51 M1reservoirCaCl2
610 mMcalcium1reservoir

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 2.25 Å / Num. obs: 16189 / % possible obs: 90 % / Num. measured all: 37651 / Rmerge(I) obs: 0.045

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Processing

SoftwareName: PROLSQ / Classification: refinement
RefinementResolution: 2.25→10 Å /
RfactorNum. reflection
obs0.197 16189
Refinement stepCycle: LAST / Resolution: 2.25→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2503 0 3 81 2587
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0190.02
X-RAY DIFFRACTIONp_angle_d0.0660.04
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.90.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it
X-RAY DIFFRACTIONp_mcangle_it
X-RAY DIFFRACTIONp_scbond_it
X-RAY DIFFRACTIONp_scangle_it
X-RAY DIFFRACTIONp_plane_restr0.0140.02
X-RAY DIFFRACTIONp_chiral_restr0.2350.15
X-RAY DIFFRACTIONp_singtor_nbd0.2140.3
X-RAY DIFFRACTIONp_multtor_nbd0.2560.3
X-RAY DIFFRACTIONp_xhyhbond_nbd0.3770.3
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor3.4473
X-RAY DIFFRACTIONp_staggered_tor23.7515
X-RAY DIFFRACTIONp_orthonormal_tor26.4120
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor
Refinement
*PLUS
Highest resolution: 2.25 Å / Lowest resolution: 10 Å / Num. reflection all: 16189
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 19.4 Å2

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