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- PDB-6k25: Crystal structure of Ca-unbound human Annexin A5 in low salt condition -

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Basic information

Entry
Database: PDB / ID: 6k25
TitleCrystal structure of Ca-unbound human Annexin A5 in low salt condition
ComponentsAnnexin A5
KeywordsLIPID BINDING PROTEIN / Annexin A5 / phospholipid binding / membrane repair / AnxA5
Function / homology
Function and homology information


phospholipase inhibitor activity / endothelial microparticle / negative regulation of coagulation / calcium-dependent phospholipid binding / vesicle membrane / phosphatidylserine binding / sarcolemma / phospholipid binding / blood coagulation / Platelet degranulation ...phospholipase inhibitor activity / endothelial microparticle / negative regulation of coagulation / calcium-dependent phospholipid binding / vesicle membrane / phosphatidylserine binding / sarcolemma / phospholipid binding / 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 repeat, conserved site / Annexin repeat signature. / Annexin / Annexin / Annexin repeats / Annexin repeat / Annexin superfamily / Annexin repeat profile.
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.401 Å
AuthorsHong, S. / Ha, N.-C.
CitationJournal: J.Struct.Biol. / Year: 2020
Title: High-resolution structures of annexin A5 in a two-dimensional array.
Authors: Hong, S. / Na, S. / Kim, O.H. / Jeong, S. / Oh, B.C. / Ha, N.C.
History
DepositionMay 13, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 25, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2023Group: 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 A5


Theoretical massNumber of molelcules
Total (without water)37,4191
Polymers37,4191
Non-polymers00
Water68538
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area15190 Å2
Unit cell
Length a, b, c (Å)94.512, 94.512, 136.701
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number182
Space group name H-MP6322
Components on special symmetry positions
IDModelComponents
11A-406-

HOH

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Components

#1: Protein Annexin A5 / Annexin-5


Mass: 37419.207 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ANXA5, ANX5 / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P08758
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 38 / 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: 2.49 Å3/Da / Density % sol: 50.56 %
Crystal growTemperature: 288 K / Method: vapor diffusion, hanging drop
Details: 0.2 M Sodium phosphate dibasic dehydrate 20% w/v Polyethylene glycol 3,350 2 mM TCEP

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Data collection

DiffractionMean temperature: 193.15 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 17, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. obs: 13961 / % possible obs: 94.8 % / Redundancy: 15.7 % / Rmerge(I) obs: 0.083 / Rpim(I) all: 0.017 / Net I/σ(I): 21.2
Reflection shellResolution: 2.4→2.44 Å / Rmerge(I) obs: 0.385 / Num. unique obs: 658 / CC1/2: 0.444 / Rpim(I) all: 0.15

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2XO3

2xo3


Resolution: 2.401→38.87 Å / SU ML: 0.37 / Cross valid method: FREE R-VALUE / σ(F): 1.57 / Phase error: 29.28
RfactorNum. reflection% reflection
Rfree0.2919 654 5.04 %
Rwork0.227 --
obs0.2302 12988 88.22 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.401→38.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2487 0 0 38 2525
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0012521
X-RAY DIFFRACTIONf_angle_d0.3993393
X-RAY DIFFRACTIONf_dihedral_angle_d6.7791540
X-RAY DIFFRACTIONf_chiral_restr0.032388
X-RAY DIFFRACTIONf_plane_restr0.002436
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4007-2.5860.36311030.291754X-RAY DIFFRACTION65
2.586-2.84620.33271460.27682403X-RAY DIFFRACTION88
2.8462-3.25790.32031260.25152633X-RAY DIFFRACTION95
3.2579-4.10380.27131220.2192604X-RAY DIFFRACTION93
4.1038-38.87550.26061570.19172940X-RAY DIFFRACTION99

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