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- PDB-2h0l: Crystal Structure of a Mutant of Rat Annexin A5 -

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Basic information

Entry
Database: PDB / ID: 2h0l
TitleCrystal Structure of a Mutant of Rat Annexin A5
ComponentsAnnexin A5
KeywordsBLOOD CLOTTING / CALCIUM / PHOSPHOLIPID MEMBRANE BINDING PROTEINS
Function / homology
Function and homology information


negative regulation of prolactin secretion / cellular response to gonadotropin-releasing hormone / regulation of flagellated sperm motility / Platelet degranulation / endothelial microparticle / cellular response to lead ion / P-type calcium transporter activity / negative regulation of blood coagulation / response to thyroid hormone / calcium-dependent phospholipid binding ...negative regulation of prolactin secretion / cellular response to gonadotropin-releasing hormone / regulation of flagellated sperm motility / Platelet degranulation / endothelial microparticle / cellular response to lead ion / P-type calcium transporter activity / negative regulation of blood coagulation / response to thyroid hormone / calcium-dependent phospholipid binding / phosphatidylserine binding / peptide hormone binding / intercalated disc / axon terminus / response to organic substance / cell projection / sarcolemma / synaptic vesicle membrane / Z disc / response to calcium ion / receptor tyrosine kinase binding / blood coagulation / synaptic vesicle / perikaryon / positive regulation of apoptotic process / external side of plasma membrane / neuronal cell body / dendrite / calcium ion binding / 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 / MOLECULAR REPLACEMENT / Resolution: 2.59 Å
AuthorsLanglois D'Estaintot, B. / Gallois, B. / Granier, T. / Tessier, B. / Brisson, A.
CitationJournal: To be Published
Title: Identification of the Residues Involved in the Formation of Annexin V Trimers within 2D and 3D Crystals
Authors: Brisson, A. / Granier, T. / Langlois D'Estaintot, B. / Gallois, B. / Tessier, B.
History
DepositionMay 15, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 19, 2007Provider: repository / Type: Initial release
Revision 1.1Oct 27, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 20, 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_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_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.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_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 30, 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

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Assembly

Deposited unit
A: Annexin A5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,7054
Polymers35,5851
Non-polymers1203
Water1,946108
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)77.918, 78.959, 60.458
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Annexin A5 / / Annexin V / Lipocortin V / Endonexin II / Calphobindin I / CBP-I / Placental anticoagulant protein ...Annexin V / Lipocortin V / Endonexin II / Calphobindin I / CBP-I / Placental anticoagulant protein I / PAP-I / PP4 / Thromboplastin inhibitor / Vascular anticoagulant-alpha / VAC-alpha / Anchorin CII


Mass: 35584.848 Da / Num. of mol.: 1 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Anxa5 / Plasmid: PET3C / Production host: Escherichia coli (E. coli) / References: UniProt: P14668
#2: Chemical ChemComp-CA / CALCIUM ION


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


Mass: 18.015 Da / Num. of mol.: 108 / 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: 2.6 Å3/Da / Density % sol: 51.9 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: PEG 4000, 300MM SODIUM ACETATA, 100MM TRIS, 3MM SODIUM AZIDE, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K, pH 8.50

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: ELLIOTT GX-21 / Wavelength: 1.5418 / Wavelength: 1.5418 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Apr 4, 2004
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.59→32.76 Å / Num. all: 10858 / Num. obs: 10858 / % possible obs: 95.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4 % / Biso Wilson estimate: 44.2 Å2 / Rsym value: 0.11 / Net I/σ(I): 6.7
Reflection shellResolution: 2.59→2.74 Å / Redundancy: 3.8 % / Mean I/σ(I) obs: 2.2 / Rsym value: 0.346 / % possible all: 96.6

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
REFMAC5.2.0005refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1A8A
Resolution: 2.59→32.76 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.872 / SU B: 25.918 / SU ML: 0.249 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 1.133 / ESU R Free: 0.365 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.278 541 4.8 %RANDOM
Rwork0.187 ---
all0.191 10731 --
obs0.191 10731 93.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 34.92 Å2
Baniso -1Baniso -2Baniso -3
1-2.59 Å20 Å20 Å2
2---1.98 Å20 Å2
3----0.61 Å2
Refinement stepCycle: LAST / Resolution: 2.59→32.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2446 0 5 106 2557
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0222485
X-RAY DIFFRACTIONr_bond_other_d0.0060.022274
X-RAY DIFFRACTIONr_angle_refined_deg1.2631.9813341
X-RAY DIFFRACTIONr_angle_other_deg0.80435273
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4885314
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.57825.043117
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.07915447
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.8081516
X-RAY DIFFRACTIONr_chiral_restr0.0640.2387
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.022776
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02483
X-RAY DIFFRACTIONr_nbd_refined0.2020.2604
X-RAY DIFFRACTIONr_nbd_other0.1830.22238
X-RAY DIFFRACTIONr_nbtor_refined0.1750.21237
X-RAY DIFFRACTIONr_nbtor_other0.0890.21292
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1820.2110
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0260.21
X-RAY DIFFRACTIONr_metal_ion_refined0.030.21
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1650.28
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1940.231
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1580.27
X-RAY DIFFRACTIONr_mcbond_it3.54831628
X-RAY DIFFRACTIONr_mcbond_other0.6893653
X-RAY DIFFRACTIONr_mcangle_it5.05162491
X-RAY DIFFRACTIONr_scbond_it2.3663980
X-RAY DIFFRACTIONr_scangle_it2.8583849
LS refinement shellResolution: 2.59→2.65 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.353 37 -
Rwork0.23 634 -
obs--95.45 %

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