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- PDB-1bcz: RECOMBINANT RAT ANNEXIN V, T72S MUTANT -

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Basic information

Entry
Database: PDB / ID: 1bcz
TitleRECOMBINANT RAT ANNEXIN V, T72S MUTANT
ComponentsANNEXIN V
KeywordsCALCIUM-BINDING PROTEIN / CALCIUM BINDING PROTEIN / PHOSPHOLIPID MEMBRANE BINDING PROTEIN
Function / homology
Function and homology information


negative regulation of prolactin secretion / cellular response to gonadotropin-releasing hormone / Platelet degranulation / cellular response to lead ion / regulation of flagellated sperm motility / endothelial microparticle / response to thyroid hormone / P-type calcium transporter activity / calcium-dependent phospholipid binding / vesicle membrane ...negative regulation of prolactin secretion / cellular response to gonadotropin-releasing hormone / Platelet degranulation / cellular response to lead ion / regulation of flagellated sperm motility / endothelial microparticle / response to thyroid hormone / P-type calcium transporter activity / calcium-dependent phospholipid binding / vesicle membrane / phosphatidylserine binding / peptide hormone binding / intercalated disc / negative regulation of blood coagulation / axon terminus / cell projection / response to calcium ion / receptor tyrosine kinase binding / sarcolemma / Z disc / blood coagulation / synaptic vesicle / synaptic vesicle membrane / 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 / DIFFERENCE FOURIER / Resolution: 2.2 Å
AuthorsMo, Y.D. / Swairjo, M.A. / Li, C.W. / Head, J.F. / Seaton, B.A.
CitationJournal: Biochemistry / Year: 1998
Title: Mutational and crystallographic analyses of interfacial residues in annexin V suggest direct interactions with phospholipid membrane components.
Authors: Campos, B. / Mo, Y.D. / Mealy, T.R. / Li, C.W. / Swairjo, M.A. / Balch, C. / Head, J.F. / Retzinger, G. / Dedman, J.R. / Seaton, B.A.
History
DepositionMay 4, 1998Processing site: BNL
Revision 1.0Nov 25, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 3, 2021Group: Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / 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_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 7, 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 V
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,0717
Polymers35,7741
Non-polymers2966
Water1,982110
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)157.390, 157.390, 37.010
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 / PLACENTAL ANTICOAGULANT PROTEIN


Mass: 35774.434 Da / Num. of mol.: 1 / Mutation: T72S
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


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.: 110 / 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: 2.47 Å3/Da / Density % sol: 50.12 %
Crystal growpH: 8.2
Details: PROTEIN CRYSTALLIZED FROM AMMONIUM SULFATE, 20MM CACL2, 50MM HEPPS, PH 8.2
Crystal grow
*PLUS
Temperature: 17 ℃ / Method: vapor diffusion
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: 293 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418
DetectorType: RIGAKU / Detector: IMAGE PLATE / Date: Feb 1, 1997
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.2→40 Å / Num. obs: 14383 / % possible obs: 84.4 % / Observed criterion σ(I): 0 / Redundancy: 2.2 % / Biso Wilson estimate: 31 Å2 / Rsym value: 0.113 / Net I/σ(I): 14.3
Reflection shellResolution: 2.2→2.28 Å / Mean I/σ(I) obs: 1.95 / Rsym value: 0.249 / % possible all: 39.9
Reflection
*PLUS
Lowest resolution: 40 Å / Num. obs: 14209 / % possible obs: 83.2 % / Redundancy: 3.5 % / Rmerge(I) obs: 0.113
Reflection shell
*PLUS
% possible obs: 39.9 % / Rmerge(I) obs: 0.249

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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: DIFFERENCE FOURIER / Resolution: 2.2→10 Å / Rfactor Rfree error: 0.011 / Data cutoff high absF: 1000000 / Data cutoff low absF: 0.001 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.299 721 4.2 %RANDOM
Rwork0.227 ---
obs0.227 14209 83.2 %-
Displacement parametersBiso mean: 30.1 Å2
Refinement stepCycle: LAST / Resolution: 2.2→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2474 0 10 106 2590
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.008
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_deg1.243
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_d0.614
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
LS refinement shellResolution: 2.2→2.3 Å / Rfactor Rfree error: 0.051 / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.359 50 35.9 %
Rwork0.342 749 -
obs--37 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMTOPHCSDX.PRO
X-RAY DIFFRACTION2
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refinement
*PLUS
Rfactor Rwork: 0.227 / Rfactor obs: 0.227 / Rfactor Rfree: 0.299
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg22.929
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg0.614
LS refinement shell
*PLUS
Rfactor Rfree: 0.359 / Rfactor Rwork: 0.342 / Rfactor obs: 0.342

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