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- PDB-1w3w: The 2.1 Angstroem resolution structure of annexin A8 -

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Basic information

Entry
Database: PDB / ID: 1w3w
TitleThe 2.1 Angstroem resolution structure of annexin A8
ComponentsANNEXIN A8
KeywordsCOAGULATION / ANNEXIN FAMILY / CALCIUM AND PHOSPHOLIPID BINDING PROTEINS
Function / homology
Function and homology information


negative regulation of phospholipase A2 activity / negative regulation of serine-type endopeptidase activity / endosome organization / calcium-dependent phospholipid binding / phosphatidylinositol-3,4-bisphosphate binding / vesicle membrane / endosomal transport / phosphatidylserine binding / phosphatidylinositol-3,4,5-trisphosphate binding / phosphatidylinositol-4,5-bisphosphate binding ...negative regulation of phospholipase A2 activity / negative regulation of serine-type endopeptidase activity / endosome organization / calcium-dependent phospholipid binding / phosphatidylinositol-3,4-bisphosphate binding / vesicle membrane / endosomal transport / phosphatidylserine binding / phosphatidylinositol-3,4,5-trisphosphate binding / phosphatidylinositol-4,5-bisphosphate binding / sarcolemma / actin filament binding / blood coagulation / late endosome membrane / : / calcium ion binding / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Annexin A8 / Annexin / Annexin repeat, conserved site / Annexin repeat signature. / Annexin / Annexin / Annexin repeats / Annexin repeat / Annexin superfamily / Annexin repeat profile. ...Annexin A8 / 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: 1.99 Å
AuthorsRety, S. / Sopkova-De Oliveira Santos, J. / Renouard, M. / Lewit-Bentley, A.
CitationJournal: J.Mol.Biol. / Year: 2005
Title: The Crystal Structure of Annexin A8 is Similar to that of Annexin A3
Authors: Rety, S. / Sopkova-De Oliveira Santos, J. / Dreyfuss, L. / Blondeau, K. / Hofbauerova, K. / Raguenes-Nicol, C. / Kerboeuf, D. / Renouard, M. / Russo-Marie, F. / Lewit-Bentley, A.
History
DepositionJul 20, 2004Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 18, 2005Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...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 / struct_conn
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.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
Revision 1.4Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ANNEXIN A8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,9672
Polymers36,9271
Non-polymers401
Water2,054114
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)50.761, 65.581, 59.229
Angle α, β, γ (deg.)90.00, 100.70, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein ANNEXIN A8 / ANNEXIN VIII / VASCULAR ANTICOAGULANT-BETA / VAC-BETA


Mass: 36927.031 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: THE N-TERMINAL 16 RESIDUES HAD BEEN CLEAVED BY PROTEOLYSIS
Source: (gene. exp.) HOMO SAPIENS (human) / Tissue: PLACENTA / Plasmid: PGEX / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: P13928
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 114 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.7 Å3/Da / Density % sol: 54.14 %
Crystal growDetails: 50MM CACODYLATE PH=6, 10MM CACL2, 45% (W/V) AMMONIUM SULPHATE

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Data collection

DiffractionMean temperature: 290 K
Diffraction sourceSource: SYNCHROTRON / Site: LURE / Beamline: DW32 / Wavelength: 0.964
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Feb 14, 2000 / Details: MULTILAYER MIRROR
RadiationMonochromator: SI 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.964 Å / Relative weight: 1
ReflectionResolution: 2.1→24 Å / Num. obs: 22712 / % possible obs: 98.5 % / Observed criterion σ(I): 0 / Redundancy: 4 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 21.7
Reflection shellResolution: 2.1→2.18 Å / Redundancy: 4 % / Rmerge(I) obs: 0.31 / Mean I/σ(I) obs: 5.52 / % possible all: 97.9

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Processing

Software
NameVersionClassification
REFMAC5.1.27refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1AXN

1axn


Resolution: 1.99→23.31 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.926 / SU B: 3.396 / SU ML: 0.095 / Cross valid method: THROUGHOUT / ESU R: 0.153 / ESU R Free: 0.144 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.218 1304 5.1 %RANDOM
Rwork0.175 ---
obs0.177 24304 97.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 22.7 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.99→23.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2445 0 1 114 2560
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0212480
X-RAY DIFFRACTIONr_bond_other_d0.0020.022265
X-RAY DIFFRACTIONr_angle_refined_deg1.141.9783334
X-RAY DIFFRACTIONr_angle_other_deg0.78835296
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4875310
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0660.2378
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022734
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02477
X-RAY DIFFRACTIONr_nbd_refined0.2050.2505
X-RAY DIFFRACTIONr_nbd_other0.2220.22359
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.0850.21472
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1760.295
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.0660.24
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1680.212
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2030.254
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3010.26
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.7461.51542
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.48822477
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.2073938
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.944.5857
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.99→2.05 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.29 106
Rwork0.221 1649

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