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- PDB-1i4a: CRYSTAL STRUCTURE OF PHOSPHORYLATION-MIMICKING MUTANT T6D OF ANNE... -

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Basic information

Entry
Database: PDB / ID: 1i4a
TitleCRYSTAL STRUCTURE OF PHOSPHORYLATION-MIMICKING MUTANT T6D OF ANNEXIN IV
ComponentsANNEXIN IV
KeywordsMETAL BINDING PROTEIN / calcium-binding / membrane-binding / phosphorylation mutant
Function / homology
Function and homology information


chondroitin sulfate binding / chromaffin granule membrane / zymogen granule membrane / calcium-dependent phospholipid binding / vesicle membrane / phosphatidylserine binding / heparin binding / carbohydrate binding / apical plasma membrane / calcium ion binding ...chondroitin sulfate binding / chromaffin granule membrane / zymogen granule membrane / calcium-dependent phospholipid binding / vesicle membrane / phosphatidylserine binding / heparin binding / carbohydrate binding / apical plasma membrane / calcium ion binding / membrane / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Annexin A4 / Annexin / Annexin repeat, conserved site / Annexin repeat signature. / Annexin / Annexin / Annexin repeats / Annexin repeat / Annexin superfamily / Annexin repeat profile. ...Annexin A4 / 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 (cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsKaetzel, M.A. / Mo, Y.D. / Mealy, T.R. / Campos, B. / Bergsma-Schutter, W. / Brisson, A. / Dedman, J.R. / Seaton, B.A.
CitationJournal: Biochemistry / Year: 2001
Title: Phosphorylation mutants elucidate the mechanism of annexin IV-mediated membrane aggregation.
Authors: Kaetzel, M.A. / Mo, Y.D. / Mealy, T.R. / Campos, B. / Bergsma-Schutter, W. / Brisson, A. / Dedman, J.R. / Seaton, B.A.
History
DepositionFeb 20, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 25, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / 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_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_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 1.4Aug 9, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / 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 IV
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,9964
Polymers35,8201
Non-polymers1763
Water4,630257
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: ANNEXIN IV
hetero molecules

A: ANNEXIN IV
hetero molecules

A: ANNEXIN IV
hetero molecules


Theoretical massNumber of molelcules
Total (without water)107,98712
Polymers107,4593
Non-polymers5299
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_545-y,x-y-1,z1
crystal symmetry operation3_655-x+y+1,-x,z1
Buried area3960 Å2
ΔGint-125 kcal/mol
Surface area40890 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)119.060, 119.060, 82.160
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 IV / ANNEXIN A4


Mass: 35819.590 Da / Num. of mol.: 1 / Mutation: T6D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (cattle) / Plasmid: PET11D / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21DE3 / References: UniProt: P13214
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 257 / 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: 3.13 Å3/Da / Density % sol: 60.68 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 5
Details: ammonium sulfate, sodium acetate, calcium chloride, pH 5.0, VAPOR DIFFUSION, temperature 298K
Crystal grow
*PLUS
Temperature: 17 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
114 mg/mlprotein1drop
220 mMcalcium1drop
320-35 %satammonium sulfate1reservoir
4100 mMsodium acetate1reservoir
50.02 %sodium azide1reservoir
62 mMdithiothreitol1reservoir
710 mM1reservoirCaCl2

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X8C
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2→50 Å / Num. all: 29310 / Num. obs: 28686 / Redundancy: 2 % / Biso Wilson estimate: 29.7225 Å2 / Rmerge(I) obs: 0.065 / Net I/σ(I): 16
Reflection
*PLUS
% possible obs: 97.9 %
Reflection shell
*PLUS
% possible obs: 99.2 % / Redundancy: 1.97 % / Rmerge(I) obs: 0.124 / Mean I/σ(I) obs: 9

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Processing

Software
NameClassification
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 1ANN

1ann


Resolution: 2→100 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2299 2798 -random
Rwork0.2039 ---
all-29310 --
obs-28309 96.6 %-
Displacement parametersBiso mean: 27.2 Å2
Refinement stepCycle: LAST / Resolution: 2→100 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2448 0 7 257 2712
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005478
X-RAY DIFFRACTIONc_angle_deg1.05354
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refinement
*PLUS
Rfactor Rfree: 0.23 / Rfactor Rwork: 0.204
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.05

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