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- PDB-2ie7: Annexin V under 2.0 MPa pressure of nitrous oxide -

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Basic information

Entry
Database: PDB / ID: 2ie7
TitleAnnexin V under 2.0 MPa pressure of nitrous oxide
ComponentsAnnexin A5
KeywordsPROTEIN AND METAL BINDING PROTEIN / calcium binding protein / phospholipid binding protein / membrane binding protein
Function / homology
Function and homology information


negative regulation of prolactin secretion / cellular response to gonadotropin-releasing hormone / Platelet degranulation / regulation of flagellated sperm motility / endothelial microparticle / cellular response to lead ion / P-type calcium transporter activity / response to thyroid hormone / calcium-dependent phospholipid binding / negative regulation of blood coagulation ...negative regulation of prolactin secretion / cellular response to gonadotropin-releasing hormone / Platelet degranulation / regulation of flagellated sperm motility / endothelial microparticle / cellular response to lead ion / P-type calcium transporter activity / response to thyroid hormone / calcium-dependent phospholipid binding / negative regulation of blood coagulation / vesicle membrane / phosphatidylserine binding / peptide hormone binding / intercalated disc / axon terminus / cell projection / sarcolemma / receptor tyrosine kinase binding / Z disc / synaptic vesicle membrane / response to calcium ion / 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
NITROUS OXIDE / Annexin A5
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.75 Å
AuthorsColloc'h, N. / Sopkova-de Oliveira Santos, J. / Prange, T. / Brisson, A. / Langlois d'Estainto, B. / Gallois, B.
CitationJournal: Biophys.J. / Year: 2007
Title: Protein Crystallography under Xenon and Nitrous Oxide Pressure: Comparison with In Vivo Pharmacology Studies and Implications for the Mechanism of Inhaled Anesthetic Action
Authors: Colloc'h, N. / Sopkova-de Oliveira Santos, J. / Retailleau, P. / Langlois d'Estainto, B. / Gallois, B. / Brisson, A. / Risso, J.J. / Lemaire, M. / Abraini, J.H.
History
DepositionSep 18, 2006Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 6, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software
Revision 1.4Oct 25, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / 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_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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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)36,41014
Polymers35,6571
Non-polymers75313
Water2,702150
1
A: Annexin A5
hetero molecules

A: Annexin A5
hetero molecules

A: Annexin A5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)109,23042
Polymers106,9723
Non-polymers2,25839
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-y+1,x-y+1,z1
crystal symmetry operation3_565-x+y,-x+1,z1
Unit cell
Length a, b, c (Å)157.028, 157.028, 37.327
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number146
Space group name H-MH3
Detailsthe biological assembly is a trimer generated from the monomer in the asymetric unit by symmetry

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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: 35657.266 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Rattus norvegicus (Norway rat) / References: UniProt: P14668
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Ca
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-N2O / NITROUS OXIDE / NITROGEN OXIDE


Mass: 44.013 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: N2O
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 150 / 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: 2.48 Å3/Da / Density % sol: 50.47 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8
Details: annexin V 10mg/ml, Tris HCL 20mM, PH 8, NACL 235MM, (NH4)SO4 1.76M, CACL2 12MM, HEPES 100MM, NAN3 3MM, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 277 K
Diffraction sourceSource: SYNCHROTRON / Site: LURE / Beamline: DW32 / Wavelength: 0.964 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Jun 17, 2003 / Details: mirrors
RadiationMonochromator: Si 111 channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.964 Å / Relative weight: 1
ReflectionResolution: 1.74→99 Å / Num. obs: 34281 / % possible obs: 97.3 % / Observed criterion σ(I): 1 / Biso Wilson estimate: 24.39 Å2 / Rmerge(I) obs: 0.045 / Χ2: 2.251 / Net I/σ(I): 29.2
Reflection shellResolution: 1.74→1.8 Å / Rmerge(I) obs: 0.178 / Num. unique all: 2953 / Χ2: 0.986 / % possible all: 83.2

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT2data extraction
MAR345345DTBdata collection
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 1A8A

1a8a


Resolution: 1.75→14.84 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.955 / SU B: 2.057 / SU ML: 0.067 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.11 / ESU R Free: 0.105 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.203 1728 5 %RANDOM
Rwork0.174 ---
obs0.175 34235 99.05 %-
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: 29.753 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å20 Å20 Å2
2---0.01 Å20 Å2
3---0.01 Å2
Refinement stepCycle: LAST / Resolution: 1.75→14.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2524 0 33 150 2707
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0222576
X-RAY DIFFRACTIONr_angle_refined_deg1.4711.9883463
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.985317
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.4424.472123
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.7915491
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.2081520
X-RAY DIFFRACTIONr_chiral_restr0.1030.2390
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021896
X-RAY DIFFRACTIONr_nbd_refined0.2090.21216
X-RAY DIFFRACTIONr_nbtor_refined0.3110.21830
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1380.2158
X-RAY DIFFRACTIONr_metal_ion_refined0.1450.210
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1650.222
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0780.27
X-RAY DIFFRACTIONr_mcbond_it1.0071.51603
X-RAY DIFFRACTIONr_mcangle_it1.72622522
X-RAY DIFFRACTIONr_scbond_it2.99531066
X-RAY DIFFRACTIONr_scangle_it4.7534.5941
LS refinement shellResolution: 1.75→1.795 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.247 126 -
Rwork0.199 2405 -
obs-2531 99.49 %

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