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- PDB-2xo2: Human Annexin V with incorporated Methionine analogue Azidohomoalanine -

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Basic information

Entry
Database: PDB / ID: 2xo2
TitleHuman Annexin V with incorporated Methionine analogue Azidohomoalanine
ComponentsANNEXIN A5
KeywordsMEMBRANE BINDING PROTEIN / POPTOSIS / ION CHANNEL
Function / homology
Function and homology information


phospholipase inhibitor activity / endothelial microparticle / negative regulation of coagulation / calcium-dependent phospholipid binding / phosphatidylserine binding / response to organic substance / phospholipid binding / sarcolemma / blood coagulation / Platelet degranulation ...phospholipase inhibitor activity / endothelial microparticle / negative regulation of coagulation / calcium-dependent phospholipid binding / phosphatidylserine binding / response to organic substance / phospholipid binding / sarcolemma / blood coagulation / Platelet degranulation / collagen-containing extracellular matrix / external side of plasma membrane / focal adhesion / calcium ion binding / negative regulation of apoptotic process / signal transduction / extracellular exosome / extracellular region / membrane / cytosol / 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 speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsDebela, M. / Merkel, L. / Goettig, P. / Budisa, N.
CitationJournal: To be Published
Title: Non-Canonical Amino Acids for Click Chemistry Reactions Incorporated in Human Annexin V
Authors: Debela, M. / Merkel, L. / Goettig, P. / Budisa, N.
History
DepositionAug 9, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 3, 2011Provider: repository / Type: Initial release
Revision 2.0Apr 24, 2019Group: Advisory / Data collection ...Advisory / Data collection / Derived calculations / Other / Polymer sequence
Category: entity_poly / pdbx_database_proc ...entity_poly / pdbx_database_proc / pdbx_database_status / pdbx_seq_map_depositor_info / pdbx_unobs_or_zero_occ_atoms / struct_conn
Item: _entity_poly.pdbx_seq_one_letter_code_can / _pdbx_database_status.recvd_author_approval ..._entity_poly.pdbx_seq_one_letter_code_can / _pdbx_database_status.recvd_author_approval / _pdbx_seq_map_depositor_info.one_letter_code / _pdbx_seq_map_depositor_info.one_letter_code_mod / _struct_conn.pdbx_leaving_atom_flag
Revision 2.1Dec 20, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_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.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 650 HELIX DETERMINATION METHOD: AUTHOR PROVIDED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ANNEXIN A5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,2797
Polymers35,9481
Non-polymers3316
Water1,964109
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)152.708, 152.708, 33.603
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3

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Components

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Protein , 1 types, 1 molecules A

#1: Protein ANNEXIN A5 / / ANNEXIN-5 / ANNEXIN V / LIPOCORTIN V / ENDONEXIN II / CALPHOBINDIN I / CBP-I / PLACENTAL ...ANNEXIN-5 / ANNEXIN V / LIPOCORTIN V / ENDONEXIN II / CALPHOBINDIN I / CBP-I / PLACENTAL ANTICOAGULANT PROTEIN I / PAP-I / PLACENTAL ANTICOAGULANT PROTEIN 4 / PP4 / THROMBOPLASTIN INHIBITOR / VASCULAR ANTICOAGULANT-ALPHA / VAC-ALPHA / ANCHORIN CII


Mass: 35948.145 Da / Num. of mol.: 1 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P08758

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Non-polymers , 5 types, 115 molecules

#2: Chemical ChemComp-CA / CALCIUM ION


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


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 109 / Source method: isolated from a natural source / Formula: H2O

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Details

Compound detailsENGINEERED RESIDUE IN CHAIN A, MET 1 TO AZH ENGINEERED RESIDUE IN CHAIN A, MET 28 TO AZH ENGINEERED ...ENGINEERED RESIDUE IN CHAIN A, MET 1 TO AZH ENGINEERED RESIDUE IN CHAIN A, MET 28 TO AZH ENGINEERED RESIDUE IN CHAIN A, MET 85 TO AZH ENGINEERED RESIDUE IN CHAIN A, MET 152 TO AZH ENGINEERED RESIDUE IN CHAIN A, MET 214 TO AZH ENGINEERED RESIDUE IN CHAIN A, MET 259 TO AZH ENGINEERED RESIDUE IN CHAIN A, MET 273 TO AZH ENGINEERED RESIDUE IN CHAIN A, MET 299 TO AZH

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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: 2.2 Å3/Da / Density % sol: 43.5 % / Description: NONE
Crystal growpH: 8.5
Details: 2.0 M AMMONIUM SULFATE, 20 MM CALCIUM CHLORIDE, 0.1 M TRIS/HCL, PH 8.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 3, 2008 / Details: DYNAMICALLY BENDABLE MIRROR
RadiationMonochromator: LN2 COOLED FIXED-EXIT SI (111) MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.8→20 Å / Num. obs: 7169 / % possible obs: 99.7 % / Observed criterion σ(I): 0 / Redundancy: 2.6 % / Biso Wilson estimate: 68.1 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 5.7
Reflection shellResolution: 2.8→2.95 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.33 / Mean I/σ(I) obs: 2.3 / % possible all: 100

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Processing

Software
NameVersionClassification
CNS1.3refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1ANX

1anx


Resolution: 2.8→19.09 Å / Rfactor Rfree error: 0.015 / Data cutoff high absF: 2742069.48 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.296 377 5.3 %RANDOM
Rwork0.274 ---
obs0.274 7158 99.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 38.1898 Å2 / ksol: 0.28 e/Å3
Displacement parametersBiso mean: 61.4 Å2
Baniso -1Baniso -2Baniso -3
1--16.73 Å20 Å20 Å2
2---16.73 Å20 Å2
3---33.45 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.6 Å0.47 Å
Luzzati d res low-5 Å
Luzzati sigma a0.83 Å0.75 Å
Refinement stepCycle: LAST / Resolution: 2.8→19.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2512 0 14 109 2635
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.1
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d22.2
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.44
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it0.461.5
X-RAY DIFFRACTIONc_mcangle_it0.862
X-RAY DIFFRACTIONc_scbond_it0.272
X-RAY DIFFRACTIONc_scangle_it0.532.5
Refine LS restraints NCSNCS model details: NONE
LS refinement shellResolution: 2.8→2.9 Å / Rfactor Rfree error: 0.086 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.445 27 3.8 %
Rwork0.413 684 -
obs--99.7 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP_MOD.PARAMPROTEIN_MOD.TOP
X-RAY DIFFRACTION2DNA-RNA_REP.PARAMDNA-RNA.TOP
X-RAY DIFFRACTION3WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION4ION.PARAMION.TOP
X-RAY DIFFRACTION5CARBOHYDRATE.PARAMCARBOHYDRATE.TOP

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