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- PDB-1g5n: ANNEXIN V COMPLEX WITH HEPARIN OLIGOSACCHARIDES -

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Basic information

Entry
Database: PDB / ID: 1g5n
TitleANNEXIN V COMPLEX WITH HEPARIN OLIGOSACCHARIDES
ComponentsANNEXIN V
KeywordsBLOOD CLOTTING / helix-bundle / membrane binding / heparin / heparan sulfate
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 / response to thyroid hormone / calcium-dependent phospholipid binding / negative regulation of blood coagulation ...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 / response to thyroid hormone / calcium-dependent phospholipid binding / negative regulation of blood coagulation / phosphatidylserine binding / peptide hormone binding / intercalated disc / axon terminus / : / cell projection / receptor tyrosine kinase binding / sarcolemma / synaptic vesicle membrane / Z disc / response to calcium ion / blood coagulation / synaptic vesicle / perikaryon / positive regulation of apoptotic process / external side of plasma membrane / neuronal cell body / calcium ion binding / dendrite / 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 / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.9 Å
AuthorsCapila, I. / Heraiz, M.J. / Mo, Y.D. / Mealy, T.R. / Campos, B. / Dedman, J.R. / Linhardt, R.J. / Seaton, B.A.
CitationJournal: Structure / Year: 2001
Title: Annexin V--heparin oligosaccharide complex suggests heparan sulfate--mediated assembly on cell surfaces.
Authors: Capila, I. / Hernaiz, M.J. / Mo, Y.D. / Mealy, T.R. / Campos, B. / Dedman, J.R. / Linhardt, R.J. / Seaton, B.A.
History
DepositionNov 1, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 6, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _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.ptnr1_symmetry / _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.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_value_order / _struct_conn.ptnr1_auth_asym_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_asym_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_conn.ptnr2_symmetry
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Feb 7, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 2.2Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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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)38,32812
Polymers35,6571
Non-polymers2,67111
Water5,098283
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)155.874, 155.874, 37.344
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


Mass: 35657.266 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: LC5 / Plasmid: PKK233-2 / Production host: Escherichia coli (E. coli) / Strain (production host): JM101 / References: UniProt: P14668
#2: Polysaccharide 4-deoxy-2-O-sulfo-alpha-L-threo-hex-4-enopyranuronic acid-(1-4)-2-deoxy-6-O-sulfo-2-(sulfoamino)- ...4-deoxy-2-O-sulfo-alpha-L-threo-hex-4-enopyranuronic acid-(1-4)-2-deoxy-6-O-sulfo-2-(sulfoamino)-alpha-D-glucopyranose-(1-4)-2-O-sulfo-alpha-L-idopyranuronic acid-(1-4)-2-deoxy-6-O-sulfo-2-(sulfoamino)-alpha-D-glucopyranose


Type: oligosaccharide / Mass: 1154.940 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
WURCS=2.0/3,4,3/[a2122h-1a_1-5_2*NSO/3=O/3=O_6*OSO/3=O/3=O][a2121A-1a_1-5_2*OSO/3=O/3=O][a21eEA-1a_1-5_2*OSO/3=O/3=O]/1-2-1-3/a4-b1_b4-c1_c4-d1WURCSPDB2Glycan 1.1.0
[][a-D-GlcpNSO36SO3]{[(4+1)][a-L-IdopA2SO3]{[(4+1)][a-D-GlcpNSO36SO3]{[(4+1)][a-L-4-deoxy-IdopA2SO3]{}}}}LINUCSPDB-CARE
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 283 / 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: 2.45 Å3/Da / Density % sol: 49.76 %
Crystal growTemperature: 290 K / Method: soaking / pH: 8.2
Details: PEG 4000, calcium chloride, HEPES buffer, pH 8.2, soaking, temperature 290.0K
Crystal grow
*PLUS
Temperature: 17 ℃ / Method: vapor diffusion / Details: Campos, B., (1998) Biochemistry, 37, 8004.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
114 mg/mlprotein1drop
220 mMcalcium1drop
334-40 %satammonium sulfate1reservoir
450 mMHEPPS1reservoir
50.02 %1reservoirNaN3
62 mMdithiothreitol1reservoir
710 mM1reservoirCaCl2

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Data collection

DiffractionMean temperature: 90 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X8C / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Sep 25, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.9→100 Å / Num. all: 26655 / Num. obs: 24078 / % possible obs: 92.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7 % / Biso Wilson estimate: 21 Å2 / Rmerge(I) obs: 0.086 / Net I/σ(I): 16.5
Reflection shellResolution: 1.9→2.02 Å / Redundancy: 3 % / Rmerge(I) obs: 0.219 / % possible all: 93.5
Reflection
*PLUS
Lowest resolution: 100 Å / Num. obs: 26655 / Num. measured all: 144885
Reflection shell
*PLUS
% possible obs: 93.5 % / Mean I/σ(I) obs: 10.5

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Processing

Software
NameClassification
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: Unpublished structure of wild-type annexin V

Resolution: 1.9→100 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: CNS
RfactorNum. reflection% reflectionSelection details
Rfree0.238 2417 -random
Rwork0.208 ---
all0.208 26655 --
obs0.208 24078 90.3 %-
Refinement stepCycle: LAST / Resolution: 1.9→100 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2504 0 149 283 2936
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONbonds0.0046
X-RAY DIFFRACTIONangles1.09
Refinement
*PLUS
Lowest resolution: 100 Å / σ(F): 0 / Rfactor obs: 0.205 / Rfactor Rfree: 0.236
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.0046
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_deg1.09

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