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- PDB-3op8: Crystal structure of the domain V from beta2-glycoprotein I -

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Basic information

Entry
Database: PDB / ID: 3op8
TitleCrystal structure of the domain V from beta2-glycoprotein I
ComponentsBeta-2-glycoprotein 1
KeywordsPROTEIN BINDING / SUSHI / antiphospholipid syndrome / anionic phospholipids binding / lipoprotein receptors binding / blood plasma
Function / homology
Function and homology information


lipoprotein lipase activator activity / triglyceride transport / platelet dense granule lumen / chylomicron / positive regulation of lipoprotein lipase activity / blood coagulation, intrinsic pathway / very-low-density lipoprotein particle / negative regulation of blood coagulation / high-density lipoprotein particle / negative regulation of myeloid cell apoptotic process ...lipoprotein lipase activator activity / triglyceride transport / platelet dense granule lumen / chylomicron / positive regulation of lipoprotein lipase activity / blood coagulation, intrinsic pathway / very-low-density lipoprotein particle / negative regulation of blood coagulation / high-density lipoprotein particle / negative regulation of myeloid cell apoptotic process / regulation of fibrinolysis / negative regulation of endothelial cell migration / triglyceride metabolic process / plasminogen activation / negative regulation of endothelial cell proliferation / negative regulation of smooth muscle cell apoptotic process / positive regulation of blood coagulation / negative regulation of fibrinolysis / negative regulation of angiogenesis / phospholipid binding / Platelet degranulation / heparin binding / collagen-containing extracellular matrix / lipid binding / cell surface / extracellular space / extracellular exosome / extracellular region / identical protein binding
Similarity search - Function
Beta-2-glycoprotein-1 fifth domain / Beta-2-glycoprotein-1 fifth domain / Complement Module, domain 1 / Complement Module; domain 1 / Sushi repeat (SCR repeat) / Domain abundant in complement control proteins; SUSHI repeat; short complement-like repeat (SCR) / Sushi/SCR/CCP domain / Sushi/SCR/CCP superfamily / Sushi/CCP/SCR domain profile. / Ribbon / Mainly Beta
Similarity search - Domain/homology
Beta-2-glycoprotein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsKolyada, A. / Lee, C.-J. / De Biasio, A. / Beglova, N.
CitationJournal: Plos One / Year: 2010
Title: A Novel Dimeric Inhibitor Targeting Beta2GPI in Beta2GPI/Antibody Complexes Implicated in Antiphospholipid Syndrome.
Authors: Kolyada, A. / Lee, C.J. / De Biasio, A. / Beglova, N.
History
DepositionAug 31, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 5, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Beta-2-glycoprotein 1
B: Beta-2-glycoprotein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,5496
Polymers19,1642
Non-polymers3844
Water1,982110
1
A: Beta-2-glycoprotein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,7743
Polymers9,5821
Non-polymers1922
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Beta-2-glycoprotein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,7743
Polymers9,5821
Non-polymers1922
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)24.290, 38.090, 49.510
Angle α, β, γ (deg.)93.83, 102.65, 90.09
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Beta-2-glycoprotein 1 / Beta-2-glycoprotein I / Beta(2)GPI / B2GPI / Apolipoprotein H / Apo-H / Activated protein C-binding ...Beta-2-glycoprotein I / Beta(2)GPI / B2GPI / Apolipoprotein H / Apo-H / Activated protein C-binding protein / APC inhibitor / Anticardiolipin cofactor


Mass: 9582.129 Da / Num. of mol.: 2 / Fragment: domain V (UNP residues 263-345)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: APOH, B2GPI / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P02749
#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 110 / 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: 2.33 Å3/Da / Density % sol: 47.13 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.2
Details: 0.1 M (NH4)2SO4, bis-Tris 0.1M, PEG 1500 40 %, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.075 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 15, 2009
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.075 Å / Relative weight: 1
ReflectionResolution: 1.7→38 Å / Num. all: 18192 / Num. obs: 17881 / % possible obs: 94 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 3 / Redundancy: 3.8 % / Rmerge(I) obs: 0.064 / Net I/σ(I): 7.8
Reflection shellResolution: 1.7→2 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.267 / Mean I/σ(I) obs: 4.5 / % possible all: 93.8

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Processing

Software
NameVersionClassification
CBASSdata collection
PHASERphasing
PHENIX(phenix.refine: 1.6.2_432)refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→38 Å / SU ML: 0.25 / σ(F): 0.06 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2186 632 5.02 %random
Rwork0.1798 ---
obs0.1819 12598 92.69 %-
all-12598 --
Solvent computationShrinkage radii: 0.77 Å / VDW probe radii: 0.9 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 48.364 Å2 / ksol: 0.478 e/Å3
Refinement stepCycle: LAST / Resolution: 1.9→38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1334 0 20 110 1464
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0161388
X-RAY DIFFRACTIONf_angle_d1.5341850
X-RAY DIFFRACTIONf_dihedral_angle_d13.165522
X-RAY DIFFRACTIONf_chiral_restr0.106195
X-RAY DIFFRACTIONf_plane_restr0.007230
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-2.04670.23891380.18462291X-RAY DIFFRACTION90
2.0467-2.25260.22391190.17242419X-RAY DIFFRACTION93
2.2526-2.57850.2531140.19162406X-RAY DIFFRACTION94
2.5785-3.24840.23271130.18412460X-RAY DIFFRACTION94
3.2484-38.00730.19641480.17442390X-RAY DIFFRACTION93

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