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- PDB-1m9i: Crystal Structure Of Phosphorylation-Mimicking Mutant T356D Of An... -

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Basic information

Entry
Database: PDB / ID: 1m9i
TitleCrystal Structure Of Phosphorylation-Mimicking Mutant T356D Of Annexin VI
ComponentsAnnexin VI
KeywordsLIPID BINDING PROTEIN / ANNEXIN / CALCIUM-BINDING / MEMBRANE-BINDING / PHOSPHORYLATION / MUTANT T356D
Function / homology
Function and homology information


negative regulation of sequestering of calcium ion / mitochondrial calcium ion homeostasis / regulation of muscle contraction / calcium-dependent phospholipid binding / vesicle membrane / ligand-gated monoatomic ion channel activity / cholesterol binding / phosphatidylserine binding / Smooth Muscle Contraction / apoptotic signaling pathway ...negative regulation of sequestering of calcium ion / mitochondrial calcium ion homeostasis / regulation of muscle contraction / calcium-dependent phospholipid binding / vesicle membrane / ligand-gated monoatomic ion channel activity / cholesterol binding / phosphatidylserine binding / Smooth Muscle Contraction / apoptotic signaling pathway / calcium-dependent protein binding / late endosome membrane / calcium ion transport / melanosome / : / monoatomic ion transmembrane transport / lysosomal membrane / focal adhesion / calcium ion binding / lipid binding / GTP binding / perinuclear region of cytoplasm / mitochondrion / extracellular exosome / identical protein 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 speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.65 Å
AuthorsFreye-Minks, C. / Kretsinger, R.H. / Creutz, C.E.
Citation
Journal: Biochemistry / Year: 2003
Title: Structural and Dynamic Changes in Human Annexin VI Induced by a Phosphorylation-Mimicking Mutation, T356D
Authors: Freye-Minks, C. / Kretsinger, R.H. / Creutz, C.E.
#1: Journal: J.Mol.Biol. / Year: 1996
Title: The structure of recombinant human annexin VI in crystals and membrane-bound
Authors: Benz, J. / Bergner, A. / Hofmann, A. / Demange, P. / Gottig, P. / Liemann, S. / Huber, R. / Voges, D.
#2: 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.
History
DepositionJul 29, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 7, 2002Provider: 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.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_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
Revision 1.5Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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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)76,0496
Polymers75,8491
Non-polymers2005
Water2,666148
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)67.970, 67.970, 204.600
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 / Lipocortin VI / P68 / P70 / PROTEIN III / Chromobindin 20 / 67 kDa calelectrin / Calphobindin-II / CPB-II


Mass: 75849.055 Da / Num. of mol.: 1 / Mutation: T356D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ANX6 / Plasmid: YepDB60 / Production host: Saccharomyces cerevisiae (brewer's yeast) / Strain (production host): DB334 / References: UniProt: P08133
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 148 / 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: 3.11 Å3/Da / Density % sol: 60.51 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 7.4
Details: 0.5M ammonium sulfate, 0.1M imidazole, pH 7.4, Vapor diffusion, temperature 298.0K
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
10.5 Msodium acetate1reservoir
20.1 Mimidazole1reservoirpH7.4
315-20 mg/mlprotein1drop

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.971 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Aug 16, 2001 / Details: Mirrors
RadiationMonochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.971 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. obs: 32036 / % possible obs: 97.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.6 % / Biso Wilson estimate: 34.7 Å2 / Rmerge(I) obs: 0.089 / Rsym value: 0.089 / Net I/σ(I): 22.8
Reflection shellResolution: 2.5→2.59 Å / Rmerge(I) obs: 0.266 / Rsym value: 0.266 / % possible all: 99.7
Reflection
*PLUS
Lowest resolution: 50 Å
Reflection shell
*PLUS
% possible obs: 99.7 %

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Processing

Software
NameClassification
HKL-2000data collection
SCALEPACKdata scaling
CNSrefinement
HKL-2000data reduction
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: human annexin VI

Resolution: 2.65→18.21 Å / Rfactor Rfree error: 0.008 / Data cutoff high rms absF: 10000 / Isotropic thermal model: restrained / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.279 1270 4.9 %random
Rwork0.225 ---
all0.243 26029 --
obs0.243 26029 97.1 %-
Displacement parametersBiso mean: 42.8 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.44 Å0.32 Å
Luzzati d res low-5 Å
Luzzati sigma a0.45 Å0.26 Å
Refinement stepCycle: LAST / Resolution: 2.65→18.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5264 0 5 148 5417
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_dihedral_angle_d19.1
X-RAY DIFFRACTIONc_improper_angle_d0.76
X-RAY DIFFRACTIONc_mcbond_it8.281.5
X-RAY DIFFRACTIONc_mcangle_it13.012
X-RAY DIFFRACTIONc_scbond_it10.262
X-RAY DIFFRACTIONc_scangle_it14.992.5
LS refinement shellResolution: 2.65→2.82 Å / Rfactor Rfree error: 0.026 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.384 223 5 %
Rwork0.281 4246 -
obs-4246 99.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.param
X-RAY DIFFRACTION3ion.param
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006901
X-RAY DIFFRACTIONc_angle_deg1.23886
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg19.1
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.76

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