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- PDB-7b01: ADAMTS13-CUB12 -

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Basic information

Entry
Database: PDB / ID: 7b01
TitleADAMTS13-CUB12
ComponentsMaltodextrin-binding protein,Maltodextrin-binding protein,Maltodextrin-binding protein,ADAMTS13 CUB12,A disintegrin and metalloproteinase with thrombospondin motifs 13,A disintegrin and metalloproteinase with thrombospondin motifs 13,A disintegrin and metalloproteinase with thrombospondin motifs 13
KeywordsHYDROLASE / ADAMTS13 / CUB / Metalloprotease
Function / homology
Function and homology information


ADAMTS13 endopeptidase / Defective B3GALTL causes PpS / glycoprotein metabolic process / O-glycosylation of TSR domain-containing proteins / Enhanced cleavage of VWF variant by ADAMTS13 / Defective VWF cleavage by ADAMTS13 variant / response to potassium ion / Platelet Adhesion to exposed collagen / peptide catabolic process / response to amine ...ADAMTS13 endopeptidase / Defective B3GALTL causes PpS / glycoprotein metabolic process / O-glycosylation of TSR domain-containing proteins / Enhanced cleavage of VWF variant by ADAMTS13 / Defective VWF cleavage by ADAMTS13 variant / response to potassium ion / Platelet Adhesion to exposed collagen / peptide catabolic process / response to amine / carbohydrate transmembrane transporter activity / cellular response to interleukin-4 / extracellular matrix organization / cell-matrix adhesion / extracellular matrix / integrin-mediated signaling pathway / protein catabolic process / protein processing / response to toxic substance / platelet activation / metalloendopeptidase activity / cellular response to type II interferon / metallopeptidase activity / blood coagulation / integrin binding / cellular response to tumor necrosis factor / outer membrane-bounded periplasmic space / cellular response to lipopolysaccharide / endoplasmic reticulum lumen / calcium ion binding / cell surface / proteolysis / extracellular space / zinc ion binding / extracellular region
Similarity search - Function
Thrombospondin type 1 domain / ADAMTS/ADAMTS-like, Spacer 1 / ADAMTS/ADAMTS-like / ADAMTS, cysteine-rich domain 2 / ADAMTS/ADAMTS-like, cysteine-rich domain 3 / ADAM-TS Spacer 1 / ADAMTS cysteine-rich domain 2 / ADAMTS cysteine-rich domain / ADAM, cysteine-rich domain / ADAM Cysteine-Rich Domain ...Thrombospondin type 1 domain / ADAMTS/ADAMTS-like, Spacer 1 / ADAMTS/ADAMTS-like / ADAMTS, cysteine-rich domain 2 / ADAMTS/ADAMTS-like, cysteine-rich domain 3 / ADAM-TS Spacer 1 / ADAMTS cysteine-rich domain 2 / ADAMTS cysteine-rich domain / ADAM, cysteine-rich domain / ADAM Cysteine-Rich Domain / Reprolysin (M12B) family zinc metalloprotease / Peptidase M12B, ADAM/reprolysin / ADAM type metalloprotease domain profile. / Spermadhesin, CUB domain superfamily / Thrombospondin type 1 domain / Thrombospondin type-1 (TSP1) repeat superfamily / Thrombospondin type-1 (TSP1) repeat profile. / Thrombospondin type 1 repeats / Thrombospondin type-1 (TSP1) repeat / Maltose/Cyclodextrin ABC transporter, substrate-binding protein / Solute-binding family 1, conserved site / Bacterial extracellular solute-binding proteins, family 1 signature. / Metallopeptidase, catalytic domain superfamily / Bacterial extracellular solute-binding protein / Bacterial extracellular solute-binding protein / Neutral zinc metallopeptidases, zinc-binding region signature.
Similarity search - Domain/homology
Maltodextrin-binding protein / A disintegrin and metalloproteinase with thrombospondin motifs 13
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsKim, H.J. / Emsley, J.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
British Heart FoundationPG/18/17/33572 United Kingdom
CitationJournal: Sci Adv / Year: 2021
Title: Crystal structure of ADAMTS13 CUB domains reveals their role in global latency.
Authors: Kim, H.J. / Xu, Y. / Petri, A. / Vanhoorelbeke, K. / Crawley, J.T.B. / Emsley, J.
History
DepositionNov 18, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 28, 2021Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Maltodextrin-binding protein,Maltodextrin-binding protein,Maltodextrin-binding protein,ADAMTS13 CUB12,A disintegrin and metalloproteinase with thrombospondin motifs 13,A disintegrin and metalloproteinase with thrombospondin motifs 13,A disintegrin and metalloproteinase with thrombospondin motifs 13
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,3093
Polymers66,5421
Non-polymers7672
Water46826
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1110 Å2
ΔGint12 kcal/mol
Surface area25120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)105.576, 105.576, 125.837
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein Maltodextrin-binding protein,Maltodextrin-binding protein,Maltodextrin-binding protein,ADAMTS13 CUB12,A disintegrin and metalloproteinase with thrombospondin motifs 13,A disintegrin and metalloproteinase with thrombospondin motifs 13,A disintegrin and metalloproteinase with thrombospondin motifs 13 / ADAM-TS 13 / ADAM-TS13 / ADAMTS-13 / von Willebrand factor-cleaving protease / vWF-CP / vWF-cleaving protease


Mass: 66542.328 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli), (gene. exp.) Homo sapiens (human)
Gene: malE, EPS91_05465, FV295_14110, NCTC8450_00456, ADAMTS13, C9orf8, UNQ6102/PRO20085
Production host: Drosophila melanogaster (fruit fly)
References: UniProt: A0A376KDN7, UniProt: Q76LX8, ADAMTS13 endopeptidase
#2: 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)][a-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#3: Polysaccharide alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose


Type: oligosaccharide / Mass: 342.297 Da / Num. of mol.: 1 / Source method: obtained synthetically
DescriptorTypeProgram
DGlcpa1-4DGlcpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1a_1-5]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][a-D-Glcp]{[(4+1)][a-D-Glcp]{}}LINUCSPDB-CARE
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 26 / 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: 3.05 Å3/Da / Density % sol: 59.73 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 21% (v/v) PEG1500, 100 mM Sodium propionate, sodium cacodylate trihydrate, 200 mM MnCl2, Bis-Tris propane, pH 5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9159 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 18, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9159 Å / Relative weight: 1
ReflectionResolution: 2.66→75.11 Å / Num. obs: 86169 / % possible obs: 92.2 % / Redundancy: 6.8 % / CC1/2: 0.99 / Net I/σ(I): 12
Reflection shellResolution: 2.66→2.7 Å / Num. unique obs: 7612 / CC1/2: 0.084

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
PDB_EXTRACT3.27data extraction
Aimlessdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6I58

6i58


Resolution: 2.8→70 Å / Cor.coef. Fo:Fc: 0.917 / Cor.coef. Fo:Fc free: 0.807 / SU B: 24.339 / SU ML: 0.436 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.627 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2917 566 4.7 %RANDOM
Rwork0.201 ---
obs0.2053 11438 58.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 171.77 Å2 / Biso mean: 55.869 Å2 / Biso min: 9.14 Å2
Baniso -1Baniso -2Baniso -3
1--0.02 Å2-0.01 Å20 Å2
2---0.02 Å20 Å2
3---0.08 Å2
Refinement stepCycle: final / Resolution: 2.8→70 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4501 0 51 26 4578
Biso mean--75.4 31.63 -
Num. residues----588
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0134662
X-RAY DIFFRACTIONr_bond_other_d0.0020.0174300
X-RAY DIFFRACTIONr_angle_refined_deg1.5051.6556337
X-RAY DIFFRACTIONr_angle_other_deg1.1531.5879992
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.8865586
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.44123.073218
X-RAY DIFFRACTIONr_dihedral_angle_3_deg22.48915750
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.0131522
X-RAY DIFFRACTIONr_chiral_restr0.0540.2619
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.025219
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02954
LS refinement shellResolution: 2.801→2.874 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.453 6 -
Rwork0.569 122 -
all-128 -
obs--8.56 %

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