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- PDB-1a8b: RAT ANNEXIN V COMPLEXED WITH GLYCEROPHOSPHOETHANOLAMINE -

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Basic information

Entry
Database: PDB / ID: 1a8b
TitleRAT ANNEXIN V COMPLEXED WITH GLYCEROPHOSPHOETHANOLAMINE
ComponentsANNEXIN VAnnexin A5
KeywordsCALCIUM BINDING PROTEIN / PHOSPHOLIPID ANALOG / MEMBRANE BINDING PROTEIN
Function / homology
Function and homology information


negative regulation of prolactin secretion / cellular response to gonadotropin-releasing hormone / regulation of flagellated sperm motility / Platelet degranulation / endothelial microparticle / cellular response to lead ion / P-type calcium transporter activity / negative regulation of blood coagulation / response to thyroid hormone / calcium-dependent phospholipid binding ...negative regulation of prolactin secretion / cellular response to gonadotropin-releasing hormone / regulation of flagellated sperm motility / Platelet degranulation / endothelial microparticle / cellular response to lead ion / P-type calcium transporter activity / negative regulation of blood coagulation / response to thyroid hormone / calcium-dependent phospholipid binding / phosphatidylserine binding / peptide hormone binding / intercalated disc / axon terminus / response to organic substance / cell projection / sarcolemma / synaptic vesicle membrane / receptor tyrosine kinase binding / Z disc / response to calcium ion / blood coagulation / synaptic vesicle / perikaryon / positive regulation of apoptotic process / external side of plasma membrane / dendrite / neuronal cell body / calcium ion binding / extracellular space / identical protein 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
L-ALPHA-GLYCEROPHOSPHORYLETHANOLAMINE / Annexin A5
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / DIFFERENCE FOURIER / Resolution: 1.9 Å
AuthorsSwairjo, M.A. / Concha, N.O. / Kaetzel, M.A. / Dedman, J.R. / Seaton, B.A.
CitationJournal: Nat.Struct.Biol. / Year: 1995
Title: Ca(2+)-bridging mechanism and phospholipid head group recognition in the membrane-binding protein annexin V.
Authors: Swairjo, M.A. / Concha, N.O. / Kaetzel, M.A. / Dedman, J.R. / Seaton, B.A.
History
DepositionMar 23, 1998Processing site: BNL
Revision 1.0Jun 17, 1998Provider: 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 V
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,29912
Polymers35,6831
Non-polymers61611
Water2,792155
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)157.470, 157.470, 37.440
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3

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Components

#1: Protein ANNEXIN V / Annexin A5 / PLACENTAL ANTICOAGULANT PROTEIN


Mass: 35683.301 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Rattus norvegicus (Norway rat) / Organ: KIDNEY / References: UniProt: P14668
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-GPE / L-ALPHA-GLYCEROPHOSPHORYLETHANOLAMINE


Mass: 215.142 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H14NO6P
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 155 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsIN THE NATIVE PROTEIN THE N-TERMINAL ALANINE IS ACETYLATED, BUT NO DENSITY IS SEEN FOR THE ...IN THE NATIVE PROTEIN THE N-TERMINAL ALANINE IS ACETYLATED, BUT NO DENSITY IS SEEN FOR THE ACETYLATION, AND THEREFORE HAS BEEN MODELLED AS ALANINE. WHILE IT IS POSSIBLE THAT THE ACETYLATION IS NOT PRESENT IN THE ACTUAL BIOLOGICAL MATERIAL USED, IT IS CERTAINLY REASONABLE TO ASSUME THAT IT IS NOT SEEN IN THE ELECTRON DENSITY MAP.

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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: 2.5 Å3/Da / Density % sol: 50.9 %
Crystal growpH: 7.1
Details: PROTEIN CRYSTALLIZED FROM AMMONIUM SULFATE, 20MM CACL2, 50MM HEPES, PH 8.2; SOAKED IN 20% PEG, 20MM CACL2, 50MM GPE, PH 7.1
Crystal grow
*PLUS
pH: 8.2 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
110-30 mg/mlprotein1drop
240-60 %ammonium sulfate1reservoir
35-10 mM1reservoirCaCl2
450 mMHEPES1reservoir
51 mMdithiothreitol1reservoir
6sodium azide1reservoir

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS / Detector: IMAGE PLATE / Date: Jul 1, 1994
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.9→44.7 Å / Num. obs: 18875 / % possible obs: 67.4 % / Observed criterion σ(I): 2 / Redundancy: 2.1 % / Rmerge(I) obs: 0.125 / Rsym value: 0.045
Reflection
*PLUS
Num. measured all: 39223

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Processing

Software
NameClassification
X-PLORrefinement
SCALEPACKdata scaling
RefinementMethod to determine structure: DIFFERENCE FOURIER / Resolution: 1.9→10 Å / σ(F): 2
RfactorNum. reflection% reflection
Rwork0.2 --
obs0.2 18688 67.4 %
Displacement parametersBiso mean: 27.7 Å2
Refinement stepCycle: LAST / Resolution: 1.9→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2506 0 23 155 2684
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.018
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg3.2
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d21.3
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.6
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARAM19X.PROTOPH19X.PRO
X-RAY DIFFRACTION2PARAM19.SOLTOPH19.SOL
X-RAY DIFFRACTION3PARAM19_CA.IONTOPH19_CA.ION
X-RAY DIFFRACTION4PARAM_GPE.ANNTOP_GPE.ANN
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg21.3
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.6

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