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- PDB-8gyc: Annexin A5 protein dimer mutant -

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ID or keywords:

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Basic information

Entry
Database: PDB / ID: 8gyc
TitleAnnexin A5 protein dimer 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: 1.8 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 22, 2022Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Oct 18, 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
B: Annexin A5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,3009
Polymers72,0192
Non-polymers2817
Water10,287571
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)69.198, 79.743, 133.936
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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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.: 2
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.: 7 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 571 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.57 Å3/Da / Density % sol: 52.06 %
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 28, 2021
RadiationMonochromator: Si111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 68560 / % possible obs: 99.9 % / Redundancy: 12.5 % / Biso Wilson estimate: 21.22 Å2 / Rmerge(I) obs: 0.145 / Rpim(I) all: 0.043 / Rrim(I) all: 0.151 / Χ2: 0.729 / Net I/σ(I): 2.7 / Num. measured all: 854364
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.8-1.8311.51.95333990.7570.592.0430.50999.8
1.83-1.8612.51.62833830.840.4691.6960.528100
1.86-1.912.81.4333960.8760.4091.4880.55199.9
1.9-1.9412.61.11333810.9010.3221.160.603100
1.94-1.9812.60.91733740.9330.2650.9550.61100
1.98-2.0312.50.72634080.9550.210.7560.63999.9
2.03-2.0812.30.61633640.960.1820.6430.69899.9
2.08-2.1311.90.48633920.970.1460.5080.70499.9
2.13-2.211.20.39433940.9780.1220.4130.75699.9
2.2-2.27130.35234170.9820.1010.3670.73399.9
2.27-2.3512.90.29834010.9860.0860.310.75499.9
2.35-2.4412.80.26234260.9890.0760.2730.751100
2.44-2.5512.70.22734090.9910.0670.2370.76999.9
2.55-2.6912.50.19434110.9920.0570.2030.79699.9
2.69-2.8611.50.1734270.9930.0520.1780.80299.7
2.86-3.0813.40.15434440.9920.0440.160.792100
3.08-3.3913.20.13134590.9960.0380.1360.832100
3.39-3.8812.70.11734920.9950.0340.1220.869100
3.88-4.8812.50.10535010.9930.0310.110.95199.6
4.88-50120.09236820.9960.0280.0960.89599.4

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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: 1.8→24.98 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 45.83 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2885 3210 4.98 %
Rwork0.2577 61287 -
obs0.2592 64497 93.66 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 127.95 Å2 / Biso mean: 26.8015 Å2 / Biso min: 8.6 Å2
Refinement stepCycle: final / Resolution: 1.8→24.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5032 0 7 571 5610
Biso mean--83.68 31.25 -
Num. residues----638
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 23

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.8-1.830.5136980.52311772187063
1.83-1.860.5155990.44472097219674
1.86-1.890.40611080.43252176228478
1.89-1.920.38121060.39752293239981
1.92-1.960.38861150.37692427254286
1.96-20.36211420.36512554269691
2-2.040.39221440.34062664280895
2.04-2.080.28291530.34592749290298
2.08-2.130.3311350.31822782291798
2.13-2.180.32931510.30732772292399
2.18-2.240.31181410.275828572998100
2.24-2.310.33511740.270227822956100
2.31-2.380.34661570.258428082965100
2.38-2.470.29921510.257628182969100
2.47-2.570.26771490.249428452994100
2.57-2.680.23831450.23528242969100
2.68-2.820.23821550.227428282983100
2.82-30.30091560.229328643020100
3-3.230.30181350.228728502985100
3.23-3.560.24841500.215328733023100
3.56-4.070.23181400.19532894303499
4.07-5.120.22281510.187729043055100
5.12-24.980.25841550.24762854300993

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