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- PDB-4jhs: Crystal structure of a C-terminal two domain fragment of human be... -

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Basic information

Entry
Database: PDB / ID: 4jhs
TitleCrystal structure of a C-terminal two domain fragment of human beta-2-glycoprotein 1
ComponentsBeta-2-glycoprotein 1
KeywordsSIGNALING PROTEIN / STRUCTURAL GENOMICS / GLYCOPROTEIN / PSI-Biology / New York Structural Genomics Research Consortium / NYSGRC / Atoms-to-Animals: The Immune Function Network / IFN
Function / homology
Function and homology information


lipoprotein lipase activator activity / triglyceride transport / platelet dense granule lumen / positive regulation of lipoprotein lipase activity / negative regulation of complement activation, classical pathway / blood coagulation, intrinsic pathway / T cell mediated immunity / negative regulation of myeloid cell apoptotic process / chylomicron / regulation of fibrinolysis ...lipoprotein lipase activator activity / triglyceride transport / platelet dense granule lumen / positive regulation of lipoprotein lipase activity / negative regulation of complement activation, classical pathway / blood coagulation, intrinsic pathway / T cell mediated immunity / negative regulation of myeloid cell apoptotic process / chylomicron / regulation of fibrinolysis / very-low-density lipoprotein particle / negative regulation of blood coagulation / high-density lipoprotein particle / 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 / plasma membrane
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/CCP/SCR domain profile. / Sushi/SCR/CCP superfamily / 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: 3 Å
AuthorsBonanno, J.B. / Toro, R. / Gizzi, A. / Chan, M.K. / Garrett-Thomson, S.C. / Patel, H. / Lim, S. / Matikainen, B. / Celikgil, A. / Garforth, S. ...Bonanno, J.B. / Toro, R. / Gizzi, A. / Chan, M.K. / Garrett-Thomson, S.C. / Patel, H. / Lim, S. / Matikainen, B. / Celikgil, A. / Garforth, S. / Hillerich, B. / Seidel, R. / Rand, J.H. / Almo, S.C. / New York Structural Genomics Research Consortium (NYSGRC) / Atoms-to-Animals: The Immune Function Network (IFN)
CitationJournal: To be Published
Title: Crystal structure of a C-terminal two domain fragment of human beta-2-glycoprotein 1
Authors: Bonanno, J.B. / Toro, R. / Gizzi, A. / Chan, M.K. / Garrett-Thomson, S.C. / Patel, H. / Lim, S. / Matikainen, B. / Celikgil, A. / Garforth, S. / Hillerich, B. / Seidel, R. / Rand, J.H. / Almo, S.C.
History
DepositionMar 5, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 24, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.2Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)21,0114
Polymers20,7221
Non-polymers2883
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)157.790, 157.790, 157.790
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number214
Space group name H-MI4132

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Components

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


Mass: 20722.479 Da / Num. of mol.: 1
Fragment: C-terminal two domain fragment (UNP residues 203-345)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: APOH, B2G1 / Plasmid: pIEx / Production host: TRICHOPLUSIA NI (cabbage looper) / Strain (production host): BTI-TN-5B1-4 / References: UniProt: P02749
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4

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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: 3.95 Å3/Da / Density % sol: 68.86 %
Crystal growTemperature: 294 K / Method: vapor diffusion / pH: 4.6
Details: 100mM sodium acetate trihydrate pH 4.6, 2.0M ammonium sulfate, vapor diffusion, temperature 294K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 19, 2011
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 3→50 Å / Num. all: 7030 / Num. obs: 7030 / % possible obs: 100 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 21.5 % / Biso Wilson estimate: 70.3 Å2 / Rsym value: 0.18 / Net I/σ(I): 16.9
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
3-3.1621.40.8191213409990.819100
3.16-3.3521.80.5141.5207689510.514100
3.35-3.5922.10.3442.3197318920.344100
3.59-3.8722.20.2333.3183428250.233100
3.87-4.2422.10.155171627770.15100
4.24-4.7421.60.1196.2151847020.119100
4.74-5.4821.10.126.1134566390.12100
5.48-6.7119.50.1146.1105285410.114100
6.71-9.4921.30.073992144330.073100
9.49-49.89818.80.0599.750882710.05999.4

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Processing

Software
NameVersionClassificationNB
SCALA3.3.20data scaling
REFMACrefinement
PDB_EXTRACT3.11data extraction
MAR345data collection
MOSFLMdata reduction
MOLREPphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1C1Z

1c1z


Resolution: 3→20 Å / WRfactor Rfree: 0.226 / WRfactor Rwork: 0.1818 / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.8611 / SU R Cruickshank DPI: 0.444 / SU Rfree: 0.3104 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2496 331 -Random
Rwork0.2066 ---
all0.2086 6987 --
obs-6984 99.95 %-
Displacement parametersBiso max: 110.96 Å2 / Biso mean: 53.8027 Å2 / Biso min: 25.75 Å2
Refinement stepCycle: LAST / Resolution: 3→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1097 0 15 0 1112
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_refined_d0.01
X-RAY DIFFRACTIONr_angle_refined_deg1.37
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.206
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.724
X-RAY DIFFRACTIONr_chiral_restr0.071
X-RAY DIFFRACTIONr_gen_planes_refined0.005
X-RAY DIFFRACTIONr_dihedral_angle_3_deg22.262
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.261
LS refinement shellResolution: 3→3.076 Å
RfactorNum. reflection% reflection
Rfree0.421 24 -
Rwork0.285 --
obs-492 100 %

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