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- PDB-6tu2: Crystal structure of rat annexin A11 -

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Basic information

Entry
Database: PDB / ID: 6tu2
TitleCrystal structure of rat annexin A11
ComponentsAnnexin
KeywordsLIPID BINDING PROTEIN / annexin / calcium / core domain
Function / homology
Function and homology information


cytokinetic process / specific granule / phosphatidylethanolamine binding / calcium-dependent phospholipid binding / S100 protein binding / azurophil granule / phagocytosis / phagocytic vesicle / spindle / response to calcium ion ...cytokinetic process / specific granule / phosphatidylethanolamine binding / calcium-dependent phospholipid binding / S100 protein binding / azurophil granule / phagocytosis / phagocytic vesicle / spindle / response to calcium ion / calcium-dependent protein binding / nuclear envelope / midbody / calcium ion binding / nucleoplasm / cytosol / cytoplasm
Similarity search - Function
Annexin A11 / Annexin repeat, conserved site / Annexin repeat signature. / Annexin / Annexin / Annexin repeats / Annexin repeat / Annexin superfamily / Annexin repeat profile.
Similarity search - Domain/homology
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsRaasakka, A. / Lillebostad, P. / Vedeler, A. / Kursula, P.
CitationJournal: Biomolecules / Year: 2020
Title: Structure of the ALS Mutation Target Annexin A11 Reveals a Stabilising N-Terminal Segment.
Authors: Lillebostad, P.A.G. / Raasakka, A. / Hjellbrekke, S.J. / Patil, S. / Rostbo, T. / Hollas, H. / Sakya, S.A. / Szigetvari, P.D. / Vedeler, A. / Kursula, P.
History
DepositionJan 1, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 6, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 18, 2020Group: Database references / Derived calculations
Category: citation / citation_author ...citation / citation_author / pdbx_struct_conn_angle / struct_conn
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _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.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_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.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _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.ptnr1_symmetry / _struct_conn.ptnr2_auth_asym_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_symmetry
Revision 1.2Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Annexin
B: Annexin
C: Annexin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)111,06513
Polymers110,6653
Non-polymers40110
Water2,972165
1
A: Annexin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,0084
Polymers36,8881
Non-polymers1203
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
B: Annexin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,0485
Polymers36,8881
Non-polymers1604
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
C: Annexin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,0084
Polymers36,8881
Non-polymers1203
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)39.070, 86.690, 87.300
Angle α, β, γ (deg.)114.000, 101.980, 97.210
Int Tables number1
Space group name H-MP1
Space group name HallP1
Symmetry operation#1: x,y,z

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Components

#1: Protein Annexin


Mass: 36888.180 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Anxa11, rCG_39189 / Production host: Escherichia coli (E. coli) / References: UniProt: Q5XI77
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 165 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.32 Å3/Da / Density % sol: 47 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5 / Details: 100 mM Bis-tris pH 5.5, 3 M NaCl

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.9763 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 12, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. obs: 42245 / % possible obs: 95.4 % / Redundancy: 3.3 % / Biso Wilson estimate: 52.7 Å2 / CC1/2: 0.992 / Rrim(I) all: 0.209 / Rsym value: 0.175 / Net I/σ(I): 5.2
Reflection shellResolution: 2.3→2.36 Å / Redundancy: 3.2 % / Mean I/σ(I) obs: 1.1 / Num. unique obs: 3046 / CC1/2: 0.476 / Rrim(I) all: 1.966 / Rsym value: 1.64 / % possible all: 95

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Processing

Software
NameVersionClassification
PHENIX1.16-3549refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1ANN

1ann


Resolution: 2.3→50 Å / Cross valid method: FREE R-VALUE
RfactorNum. reflection% reflection
Rfree0.266 -5 %
Rwork0.2282 --
obs0.23 42147 95.4 %
Displacement parametersBiso mean: 48.41 Å2
Refinement stepCycle: LAST / Resolution: 2.3→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7422 0 10 165 7597
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0027500
X-RAY DIFFRACTIONf_angle_d0.430210035
X-RAY DIFFRACTIONf_chiral_restr0.03131128
X-RAY DIFFRACTIONf_plane_restr0.00181302
X-RAY DIFFRACTIONf_dihedral_angle_d14.39514662

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