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- PDB-1n41: Crystal Structure of Annexin V K27E Mutant -

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Basic information

Entry
Database: PDB / ID: 1n41
TitleCrystal Structure of Annexin V K27E Mutant
Componentsannexin VAnnexin A5
KeywordsLIPID BINDING PROTEIN / calcium / phospholipid 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
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 2.1 Å
AuthorsMo, Y.D. / Campos, B. / Mealy, T.R. / Commodore, L. / Head, J.F. / Dedman, J.R. / Seaton, B.A.
CitationJournal: J.Biol.Chem. / Year: 2003
Title: Interfacial basic cluster in annexin V couples phospholipid binding and trimer formation on membrane surfaces
Authors: Mo, Y.D. / Campos, B. / Mealy, T.R. / Commodore, L. / Head, J.F. / Dedman, J.R. / Seaton, B.A.
History
DepositionOct 30, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 4, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: 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.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
Revision 1.4Feb 14, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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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)36,2779
Polymers35,7881
Non-polymers4898
Water3,513195
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)157.596, 157.596, 37.059
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 / lipocortin-V


Mass: 35788.395 Da / Num. of mol.: 1 / Mutation: K27E
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Plasmid: PKK233-2 / Production host: Escherichia coli (E. coli) / Strain (production host): JM101 / References: UniProt: P14668
#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 / Sulfate


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 195 / 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: 2.33 Å3/Da / Density % sol: 46.72 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 8.2
Details: ammonium sulfate, CaCl2, pH 8.2, VAPOR DIFFUSION, SITTING DROP, temperature 290K
Crystal grow
*PLUS
Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
134-40 %satammonium sulfate1reservoir
250 mMHEPES1reservoirpH8.2
32 mMdithiothreitol1reservoir
410 mM1reservoirCaCl2
514 mg/mlprotein1drop
620 mM1dropCaCl2

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IIC / Detector: IMAGE PLATE
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. all: 23159 / Num. obs: 21924 / % possible obs: 95 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.064
Reflection shellResolution: 2→2.07 Å / Rmerge(I) obs: 0.234 / % possible all: 76.4
Reflection
*PLUS
Lowest resolution: 50 Å / % possible obs: 96.7 %
Reflection shell
*PLUS
% possible obs: 92 % / Rmerge(I) obs: 0.236

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
CNSphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 2.1→50 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.2234 1916 random
Rwork0.187 --
all0.187 20019 -
obs0.187 19384 -
Refinement stepCycle: LAST / Resolution: 2.1→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2504 0 20 195 2719
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg0.005531
X-RAY DIFFRACTIONc_bond_d1.10184
Refinement
*PLUS
Lowest resolution: 50 Å / Rfactor obs: 0.187
Solvent computation
*PLUS
Displacement parameters
*PLUS

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