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- PDB-1qub: CRYSTAL STRUCTURE OF THE GLYCOSYLATED FIVE-DOMAIN HUMAN BETA2-GLY... -

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Basic information

Entry
Database: PDB / ID: 1qub
TitleCRYSTAL STRUCTURE OF THE GLYCOSYLATED FIVE-DOMAIN HUMAN BETA2-GLYCOPROTEIN I PURIFIED FROM BLOOD PLASMA
ComponentsPROTEIN (human beta2-Glycoprotein I)
KeywordsMEMBRANE ADHESION / SHORT CONSENSUS REPEAT / SUSHI / COMPLEMENT CONTROL PROTEIN / N-GLYCOSYLATION / MULTI-DOMAIN
Function / homology
Function and homology information


triglyceride transport / lipoprotein lipase activator activity / platelet dense granule lumen / positive regulation of lipoprotein lipase activity / blood coagulation, intrinsic pathway / negative regulation of myeloid cell apoptotic process / regulation of fibrinolysis / chylomicron / high-density lipoprotein particle / very-low-density lipoprotein particle ...triglyceride transport / lipoprotein lipase activator activity / platelet dense granule lumen / positive regulation of lipoprotein lipase activity / blood coagulation, intrinsic pathway / negative regulation of myeloid cell apoptotic process / regulation of fibrinolysis / chylomicron / high-density lipoprotein particle / very-low-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 / negative regulation of blood coagulation / positive regulation of blood coagulation / negative regulation of fibrinolysis / negative regulation of angiogenesis / phospholipid binding / Platelet degranulation / heparin binding / : / 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/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 / MIRAS / Resolution: 2.7 Å
AuthorsBouma, B. / de Groot, P.G. / van den Elsen, J.M.H. / Ravelli, R.B.G. / Schouten, A. / Simmelink, M.J.A. / Derksen, R.H.W.M. / Kroon, J. / Gros, P.
CitationJournal: EMBO J. / Year: 1999
Title: Adhesion mechanism of human beta(2)-glycoprotein I to phospholipids based on its crystal structure.
Authors: Bouma, B. / de Groot, P.G. / van den Elsen, J.M. / Ravelli, R.B. / Schouten, A. / Simmelink, M.J. / Derksen, R.H. / Kroon, J. / Gros, P.
History
DepositionJul 1, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 8, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Jan 24, 2018Group: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / database_PDB_caveat / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_validate_chiral / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_validate_chiral.auth_asym_id / _pdbx_validate_chiral.auth_seq_id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_comp_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Oct 30, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PROTEIN (human beta2-Glycoprotein I)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,9325
Polymers35,4791
Non-polymers1,4534
Water57632
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)161.170, 166.490, 114.510
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein PROTEIN (human beta2-Glycoprotein I)


Mass: 35478.641 Da / Num. of mol.: 1 / Fragment: BETA2-GLYCOPROTEIN I / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Organelle: BLOOD PLASMA / References: UniProt: P02749
#2: Polysaccharide alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 586.542 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1a_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}}LINUCSPDB-CARE
#3: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][a-D-GlcpNAc]{}}}LINUCSPDB-CARE
#4: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 32 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 8.5 Å3/Da / Density % sol: 86 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 1.5 M ammonium sulphate 20 mM cadmium chloride 2 % (v/v) glycerol 100 mM HEPES 1.5 M AMMONIUM PHOSPHATE 100 MM SODIUM ACETATE, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal
*PLUS
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 7.3
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
16.5 mg/mlprotein1drop
2150 mM1dropNaCl
350 mMTris-HCl1drop
41.5 Mammonium sulfate1reservoir
52 %(v/v)glycerol1reservoir
620 mM1reservoirCdCl2
70.1 MHEPES1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9354
DetectorType: ADSC / Detector: CCD / Date: Sep 27, 1998 / Details: TOROIDAL MIRROR
RadiationMonochromator: SI(333) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9354 Å / Relative weight: 1
ReflectionResolution: 2.7→40 Å / Num. all: 42497 / Num. obs: 42497 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 3.8 % / Biso Wilson estimate: 46.7 Å2 / Rmerge(I) obs: 0.089 / Rsym value: 0.089 / Net I/σ(I): 5.8
Reflection shellResolution: 2.7→2.85 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.363 / Mean I/σ(I) obs: 2 / Num. unique all: 6122 / Rsym value: 0.364 / % possible all: 99.6
Reflection
*PLUS
Reflection shell
*PLUS
% possible obs: 99.6 %

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
TRUNCATEdata reduction
SOLVEphasing
CNSrefinement
CCP4(TRUNCATE)data scaling
RefinementMethod to determine structure: MIRAS / Resolution: 2.7→40 Å / Rfactor Rfree error: 0.006 / Rfactor Rfree error details: 0.006 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: Used maximum likelihood target using amplitudes
RfactorNum. reflection% reflectionSelection details
Rfree0.269 2082 4.9 %random
Rwork0.249 ---
all0.25 42451 --
obs0.25 42451 99.7 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 34.7939 Å2 / ksol: 0.371246 e/Å3
Displacement parametersBiso mean: 51.2 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.44 Å0.41 Å
Luzzati d res low-40 Å
Luzzati sigma a0.37 Å0.39 Å
Refinement stepCycle: LAST / Resolution: 2.7→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2480 0 95 32 2607
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.019
X-RAY DIFFRACTIONc_angle_deg1.9
X-RAY DIFFRACTIONc_dihedral_angle_d25.3
X-RAY DIFFRACTIONc_improper_angle_d1.35
X-RAY DIFFRACTIONc_mcbond_it1.651.5
X-RAY DIFFRACTIONc_mcangle_it2.822
X-RAY DIFFRACTIONc_scbond_it3.412
X-RAY DIFFRACTIONc_scangle_it4.82.5
LS refinement shellResolution: 2.7→2.87 Å / Rfactor Rfree error: 0.02 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.399 363 5.2 %
Rwork0.399 6631 -
obs--100 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2CARBOHYDRATE.PARAMCARBOHYDRATE.TOP
X-RAY DIFFRACTION3WATER_REP.PARAMWATER.TOP
Software
*PLUS
Name: CNS / Classification: refinement
Refinement
*PLUS
Lowest resolution: 40 Å / σ(F): 0 / % reflection Rfree: 4.9 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 51.2 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.019
X-RAY DIFFRACTIONc_angle_deg1.9
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg25.3
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.35
X-RAY DIFFRACTIONc_mcbond_it1
X-RAY DIFFRACTIONc_scbond_it2
X-RAY DIFFRACTIONc_mcangle_it2
X-RAY DIFFRACTIONc_scangle_it2.5
LS refinement shell
*PLUS
Rfactor Rfree: 0.399 / % reflection Rfree: 5.2 % / Rfactor Rwork: 0.399

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