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- PDB-8h0j: Annexin A5 mutant -

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Basic information

Entry
Database: PDB / ID: 8h0j
TitleAnnexin A5 mutant
ComponentsAnnexin A5
KeywordsLIPID BINDING PROTEIN / calcium-binding / apoptosis-detection
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: 2.23 Å
AuthorsHua, Z.C. / Tang, W.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)81630092 China
CitationJournal: To Be Published
Title: structure dissection of the membrane aggregation mechanism induced by Annexin A5 mutation
Authors: Hua, Z.C. / Tang, W.
History
DepositionSep 29, 2022Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Oct 4, 2023Provider: repository / Type: Initial release

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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)36,2106
Polymers36,0101
Non-polymers2005
Water3,459192
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area400 Å2
ΔGint-45 kcal/mol
Surface area15000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.294, 134.470, 79.227
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Annexin A5 / Anchorin CII / Annexin V / Annexin-5 / Calphobindin I / CPB-I / Endonexin II / Lipocortin V / ...Anchorin CII / Annexin V / Annexin-5 / Calphobindin I / CPB-I / Endonexin II / Lipocortin V / Placental anticoagulant protein 4 / PP4 / Placental anticoagulant protein I / PAP-I / Thromboplastin inhibitor / Vascular anticoagulant-alpha / VAC-alpha


Mass: 36009.703 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ANXA5, ANX5, ENX2, PP4 / Production host: Escherichia coli (E. coli) / References: UniProt: P08758
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 192 / 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: 2.56 Å3/Da / Density % sol: 52 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion, hanging drop
Details: PEG 3350, sodium chloride, 2-[4-(2-hydroxyethyl)piperazin-1-yl]ethanesulfonic acid

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.987 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 1, 2021
RadiationMonochromator: Si111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 2.23→30 Å / Num. obs: 18237 / % possible obs: 100 % / Redundancy: 12.4 % / Biso Wilson estimate: 36.76 Å2 / Rmerge(I) obs: 0.166 / Rpim(I) all: 0.049 / Rrim(I) all: 0.173 / Χ2: 0.749 / Net I/σ(I): 3.2
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.25-2.2991.0188840.6990.3491.0790.49999.8
2.29-2.339.90.98950.7290.2940.9490.52599.7
2.33-2.3811.80.8038950.8410.2410.8390.527100
2.38-2.4212.30.7148950.910.210.7450.499100
2.42-2.4812.70.6648990.9110.1930.6920.488100
2.48-2.5312.90.6079040.9520.1750.6320.516100
2.53-2.6130.5098930.9510.1460.530.53100
2.6-2.67130.4759180.9390.1360.4950.526100
2.67-2.7512.60.3818990.9630.1110.3970.574100
2.75-2.8311.90.359100.9690.1060.3660.583100
2.83-2.9413.40.3059010.9790.0860.3170.587100
2.94-3.0513.60.2669050.9850.0740.2760.617100
3.05-3.1913.40.2169070.9870.0610.2250.735100
3.19-3.3613.40.1719050.990.0490.1780.769100
3.36-3.5712.80.1459110.9890.0420.1510.868100
3.57-3.8512.40.1249200.9930.0360.131.048100
3.85-4.2313.60.1069330.9950.030.111.121100
4.23-4.8413.20.0979170.9960.0270.11.102100
4.84-6.0912.20.0929480.9950.0270.0960.9199.9
6.09-3011.70.1069980.9940.0330.1111.733100

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIX1.19.2_4158refinement
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1AVH

1avh


Resolution: 2.23→25.63 Å / SU ML: 0.27 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 25.73 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2465 926 5.09 %
Rwork0.1877 17262 -
obs0.1907 18188 98.55 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 106.62 Å2 / Biso mean: 44.592 Å2 / Biso min: 20.02 Å2
Refinement stepCycle: final / Resolution: 2.23→25.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2516 0 5 192 2713
Biso mean--77.61 44.62 -
Num. residues----319
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 7

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.23-2.350.29011280.23562221234991
2.35-2.490.29441300.228324772607100
2.49-2.680.32391220.217424692591100
2.69-2.950.28241310.212724812612100
2.96-3.380.28481400.201224852625100
3.38-4.260.22451440.166825132657100
4.26-25.630.1961310.16542616274799

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