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- PDB-6k22: Crystal structure of Ca-bound human Annexin A5 in low salt condition -

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Basic information

Entry
Database: PDB / ID: 6k22
TitleCrystal structure of Ca-bound 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: 2.747 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,5394
Polymers37,4191
Non-polymers1203
Water68538
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area100 Å2
ΔGint-12 kcal/mol
Surface area14890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.795, 92.795, 134.055
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number182
Space group name H-MP6322

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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: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca
#3: 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: 2.22 Å3/Da / Density % sol: 44.71 %
Crystal growTemperature: 287 K / Method: vapor diffusion, hanging drop
Details: 0.2 M Potassium Citrate Tribasic pH 8.3 0.1 M HEPES pH 7.5 17% PEG3350 50uM CaCl2 2mM 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: 1.2325 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 30, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.2325 Å / Relative weight: 1
ReflectionResolution: 2.747→50 Å / Num. obs: 9341 / % possible obs: 98.8 % / Redundancy: 16.8 % / Rmerge(I) obs: 0.145 / Rpim(I) all: 0.032 / Rrim(I) all: 0.149 / Χ2: 0.981 / Net I/σ(I): 14.8
Reflection shellResolution: 2.75→2.8 Å / Redundancy: 7.4 % / Rmerge(I) obs: 0.39 / Mean I/σ(I) obs: 3.5 / Num. unique obs: 411 / CC1/2: 0.35 / Rpim(I) all: 0.134 / Rrim(I) all: 0.415 / % possible all: 87.4

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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: 2.747→46.397 Å / SU ML: 0.41 / Cross valid method: FREE R-VALUE / σ(F): 1.58 / Phase error: 28.41
RfactorNum. reflection% reflection
Rfree0.306 445 5.01 %
Rwork0.2503 --
obs0.253 8874 94.03 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.747→46.397 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2496 0 3 38 2537
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0022530
X-RAY DIFFRACTIONf_angle_d0.4113405
X-RAY DIFFRACTIONf_dihedral_angle_d5.0471546
X-RAY DIFFRACTIONf_chiral_restr0.03389
X-RAY DIFFRACTIONf_plane_restr0.002438
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.747-3.14440.35531290.30372368X-RAY DIFFRACTION82
3.1444-3.96130.32561600.2642934X-RAY DIFFRACTION100
3.9613-46.40410.27161560.22293127X-RAY DIFFRACTION100

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