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- PDB-6xst: Recombinant Beta-2-Glycoprotein I with putative membrane insertio... -

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Basic information

Entry
Database: PDB / ID: 6xst
TitleRecombinant Beta-2-Glycoprotein I with putative membrane insertion loop
ComponentsBeta-2-glycoprotein 1
KeywordsBLOOD CLOTTING / Plasma protein / antibody binding / antiphospholipid syndrome
Function / homology
Function and homology information


positive regulation of triglyceride metabolic process / triglyceride transport / lipoprotein lipase activator activity / chylomicron remodeling / platelet dense granule lumen / lipase binding / blood coagulation, intrinsic pathway / very-low-density lipoprotein particle remodeling / regulation of fibrinolysis / negative regulation of myeloid cell apoptotic process ...positive regulation of triglyceride metabolic process / triglyceride transport / lipoprotein lipase activator activity / chylomicron remodeling / platelet dense granule lumen / lipase binding / blood coagulation, intrinsic pathway / very-low-density lipoprotein particle remodeling / regulation of fibrinolysis / negative regulation of myeloid cell apoptotic process / chylomicron / high-density lipoprotein particle / very-low-density lipoprotein particle / negative regulation of endothelial cell migration / 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 / 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
Similarity search - Domain/homology
Beta-2-glycoprotein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.92 Å
AuthorsKlenotic, P.A. / Yu, E.W.Y.
CitationJournal: To Be Published
Title: Beta-2-Glycoprotein I and it's role in APS
Authors: Klenotic, P.A. / Yu, E.W.Y.
History
DepositionJul 16, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 21, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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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)38,0455
Polymers36,3001
Non-polymers1,7464
Water00
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)159.188, 175.225, 113.170
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 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 / Beta(2)GPI


Mass: 36299.594 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: APOH, B2G1 / Cell line (production host): HEK293 / Production host: Homo sapiens (human) / References: UniProt: P02749
#2: Polysaccharide alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1- ...alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 732.682 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-4DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,4,3/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1a_1-5][a1221m-1a_1-5]/1-1-2-3/a4-b1_a6-d1_b4-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][a-D-Manp]{}}[(6+1)][a-L-Fucp]{}}}LINUCSPDB-CARE
#3: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 570.542 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5]/1-1-2/a4-b1_a6-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}[(6+1)][a-L-Fucp]{}}}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
Has ligand of interestN
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

Crystal growMethod: vapor diffusion, hanging drop / Details: 100mM Hepes, pH 7.5, 1.8M Ammonium Sulfate

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Data collection

DiffractionMean temperature: 277 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 9, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.91→100 Å / Num. obs: 34541 / % possible obs: 99.7 % / Redundancy: 7.3 % / Rmerge(I) obs: 0.206 / Rpim(I) all: 0.081 / Rrim(I) all: 0.222 / Χ2: 1 / Net I/σ(I): 3.8 / Num. measured all: 253404
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.91-3.017.22.6134270.2011.0372.812199.9
3.01-3.137.11.75934100.4010.7031.8980.99899.4
3.13-3.287.71.17433980.6890.4471.2581.00299.9
3.28-3.457.50.74534170.8580.2860.7991.00299.9
3.45-3.677.30.43334320.9350.1690.4650.99999.9
3.67-3.957.10.27934300.9640.110.30.99899.3
3.95-4.357.70.17834570.9870.0670.191100
4.35-4.987.20.12734470.990.050.1360.99899.5
4.98-6.277.60.09935100.9940.0380.1060.99799.9
6.27-10070.06236130.9980.0250.0671.00199.4

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
PDB_EXTRACT3.25data extraction
Cootmodel building
HKL-2000data scaling
PHENIXphasing
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1QUB

1qub


Resolution: 2.92→87.61 Å / SU ML: 0.48 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 27.83 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2387 1998 5.79 %
Rwork0.2255 32497 -
obs0.2263 34495 99.15 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 189.82 Å2 / Biso mean: 88.6605 Å2 / Biso min: 30 Å2
Refinement stepCycle: final / Resolution: 2.92→87.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2531 0 115 0 2646
Biso mean--134.46 --
Num. residues----326
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.92-2.990.38151310.3962134226593
2.99-3.070.37031410.3722290243199
3.07-3.160.34991430.36823172460100
3.16-3.260.32511420.318723092451100
3.26-3.380.28391430.289923052448100
3.38-3.520.31841410.258723072448100
3.52-3.680.23141430.235423172460100
3.68-3.870.25621420.22482322246499
3.87-4.110.19421420.190423222464100
4.11-4.430.18641450.168823472492100
4.43-4.880.18471440.164523402484100
4.88-5.580.17281440.16712344248899
5.58-7.030.22491470.206623822529100
7.03-87.610.26351500.24482461261199
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.30091.25020.87170.5944-0.05354.6337-0.25420.16640.1532-0.15550.2905-0.1462-0.84680.64600.6713-0.04560.0070.62490.04440.6601167.246160.441492.0698
21.19980.0496-0.14730.69371.05134.0132-0.0358-0.0780.0849-0.1217-0.0131-0.049-0.16280.190300.6182-0.1549-0.02910.71330.02710.7583174.3271197.7462120.2379
31.93321.7343.06740.58331.44340.83540.1109-0.64390.0617-0.0153-0.40680.03560.1057-0.5228-0.00070.9605-0.3692-0.02171.2817-0.1870.9278193.6251224.0093154.675
42.7036-2.2025-2.66852.72822.14334.25590.0323-0.0139-0.0159-0.249-0.1454-0.46560.48160.4500.8466-0.04780.0120.85320.04540.8552235.2547231.1345153.1088
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 61 )A1 - 61
2X-RAY DIFFRACTION2chain 'A' and (resid 62 through 149 )A62 - 149
3X-RAY DIFFRACTION3chain 'A' and (resid 150 through 240 )A150 - 240
4X-RAY DIFFRACTION4chain 'A' and (resid 241 through 326 )A241 - 326

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