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- PDB-1avc: BOVINE ANNEXIN VI (CALCIUM-BOUND) -

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Basic information

Entry
Database: PDB / ID: 1avc
TitleBOVINE ANNEXIN VI (CALCIUM-BOUND)
ComponentsANNEXIN VI
KeywordsCALCIUM/PHOSPHOLIPID-BINDING PROTEIN / ANNEXIN / CALCIUM-BINDING / MEMBRANE-BINDING / CALCIUM-PHOSPHOLIPID-BINDING PROTEIN complex
Function / homology
Function and homology information


negative regulation of sequestering of calcium ion / growth plate cartilage chondrocyte differentiation / chondroitin sulfate binding / biomineral tissue development / chromaffin granule membrane / mitochondrial calcium ion homeostasis / regulation of muscle contraction / calcium-dependent phospholipid binding / calcium ion import / vesicle membrane ...negative regulation of sequestering of calcium ion / growth plate cartilage chondrocyte differentiation / chondroitin sulfate binding / biomineral tissue development / chromaffin granule membrane / mitochondrial calcium ion homeostasis / regulation of muscle contraction / calcium-dependent phospholipid binding / calcium ion import / vesicle membrane / cargo receptor activity / phosphatidylserine binding / mitochondrial crista / stress fiber / apoptotic signaling pathway / calcium ion transmembrane transport / calcium channel activity / calcium-dependent protein binding / actin filament binding / calcium ion transport / melanosome / heparin binding / vesicle / focal adhesion / calcium ion binding / perinuclear region of cytoplasm / enzyme binding / nucleus / membrane / plasma membrane / cytoplasm
Similarity search - Function
Annexin A6 / Annexin / Annexin repeat, conserved site / Annexin repeat signature. / Annexin / Annexin / Annexin repeats / Annexin repeat / Annexin superfamily / Annexin repeat profile. ...Annexin A6 / 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 speciesBos taurus (domestic cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsAvila-Sakar, A.J. / Creutz, C.E. / Kretsinger, R.H.
Citation
Journal: Biochim.Biophys.Acta / Year: 1998
Title: Crystal structure of bovine annexin VI in a calcium-bound state.
Authors: Avila-Sakar, A.J. / Creutz, C.E. / Kretsinger, R.H.
#1: Journal: Biochim.Biophys.Acta / Year: 1996
Title: The Crystal Structure of Annexin Vi Indicates Relative Rotation of the Two Lobes Upon Membrane Binding
Authors: Kawasaki, H. / Avila-Sakar, A. / Creutz, C.E. / Kretsinger, R.H.
History
DepositionSep 16, 1997Processing site: BNL
Revision 1.0Jan 28, 1998Provider: 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 ...Database references / Derived calculations / Other / Refinement description
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_initial_refinement_model / 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_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_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 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ANNEXIN VI
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,2527
Polymers76,0121
Non-polymers2406
Water2,108117
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)67.404, 67.404, 200.078
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number78
Space group name H-MP43

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Components

#1: Protein ANNEXIN VI / P68 / PROTEIN III / 67-KDA-CALCIMEDIN / LIPOCORTIN VI / 67-KDA-CALELECTRIN / CHROMOBINDIN 20 / CALPHOBINDIN II


Mass: 76011.500 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / Cellular location: MEMBRANE-PERIPHERAL / Organ: LIVER / References: UniProt: P79134
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 117 / 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: 2.99 Å3/Da / Density % sol: 39.7 % / Description: PROBE ~1/2 THE MASS OF ANNEXIN VI
Crystal growMethod: vapor diffusion, hanging drop / pH: 6.5
Details: VAPOUR DIFFUSION (HANGING DROP), SODIUM ACETATE 1.2 M AS PRECIPITANT, POTASSIUM CACODYLATE 0.1 M, PH 6.5, CALCIUM CHLORIDE 6.2 MM ROOM TEMPERATURE, vapor diffusion - hanging drop
Temp details: room temp
Crystal grow
*PLUS
pH: 6.7 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
12.5 mg/mlprotein1drop
20.2 MNa acetate1drop
30.02 MNa-cacodylate1drop
41.04 mM1dropCaCl2
50.11 mM1dropCa2+
61.2 MNa-acetate1reservoir
70.1 MNa-cacodylate1reservoir
86.25 mM1reservoirCaCl2
90.660 mM1reservoirCa2+

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 1.0093
DetectorType: FUJI / Detector: IMAGE PLATE / Date: Apr 14, 1996 / Details: MIRRORS
RadiationMonochromator: SI(111) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0093 Å / Relative weight: 1
ReflectionResolution: 2.5→30 Å / Num. obs: 30424 / % possible obs: 98.6 % / Redundancy: 3.8 % / Biso Wilson estimate: 45.7 Å2 / Rmerge(I) obs: 0.066 / Rsym value: 0.066 / Net I/σ(I): 20.7
Reflection shellResolution: 2.5→2.6 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.307 / Mean I/σ(I) obs: 4.6 / Rsym value: 0.307 / % possible all: 99.3
Reflection
*PLUS
Highest resolution: 2.9 Å / Lowest resolution: 10 Å / Num. obs: 19075 / % possible obs: 98.7 % / Rmerge(I) obs: 0.05
Reflection shell
*PLUS
Highest resolution: 2.9 Å / Lowest resolution: 3 Å / % possible obs: 99.6 % / Redundancy: 3.8 % / Num. unique obs: 1912 / Rmerge(I) obs: 0.137 / Mean I/σ(I) obs: 9.8

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Processing

Software
NameVersionClassification
X-PLOR3.851model building
X-PLOR3.851refinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLOR3.851phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: BOVINE ANNEXIN VI: PDB ENTRY 1ANN

1ann


Resolution: 2.9→10 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.1 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / Details: BULK SOLVENT B=62.4 A**2, K=0.48
RfactorNum. reflection% reflectionSelection details
Rfree0.268 -6 %RANDOM
Rwork0.205 ---
obs0.205 18978 98.7 %-
Displacement parametersBiso mean: 28.3 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.54 Å0.4 Å
Luzzati d res low-10 Å
Luzzati sigma a0.27 Å0.23 Å
Refinement stepCycle: LAST / Resolution: 2.9→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5231 0 6 117 5354
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.003
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_deg0.7
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d22.9
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d0.4
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it2.991.5
X-RAY DIFFRACTIONx_mcangle_it3.912
X-RAY DIFFRACTIONx_scbond_it4.092
X-RAY DIFFRACTIONx_scangle_it5.482.5
LS refinement shellResolution: 2.9→3 Å / Rfactor Rfree error: 0.028 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.327 -5.9 %
Rwork0.284 1783 -
obs--99.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMTOPCSDX.PRO
X-RAY DIFFRACTION2PARAMETER.ELEMENTSTOP19.SOL
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refinement
*PLUS
Num. reflection obs: 17821 / Num. reflection Rfree: 1157 / Rfactor obs: 0.204
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg22.9
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg0.4
LS refinement shell
*PLUS
Rfactor Rfree: 0.329 / Rfactor obs: 0.285

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