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Entry
Database: PDB / ID: 3vn4
TitleCrystal structure of the exosite-containing fragment of human ADAMTS13 (P475S mutant)
ComponentsA disintegrin and metalloproteinase with thrombospondin motifs 13
KeywordsHYDROLASE
Function / homology
Function and homology information


ADAMTS13 endopeptidase / glycoprotein metabolic process / Defective B3GALTL causes PpS / O-glycosylation of TSR domain-containing proteins / response to potassium ion / peptide catabolic process / response to amine / cellular response to interleukin-4 / extracellular matrix organization / cell-matrix adhesion ...ADAMTS13 endopeptidase / glycoprotein metabolic process / Defective B3GALTL causes PpS / O-glycosylation of TSR domain-containing proteins / response to potassium ion / peptide catabolic process / response to amine / 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 / metalloendopeptidase activity / platelet activation / cellular response to type II interferon / metallopeptidase activity / integrin binding / cellular response to tumor necrosis factor / cellular response to lipopolysaccharide / endoplasmic reticulum lumen / calcium ion binding / cell surface / proteolysis / extracellular space / zinc ion binding
Similarity search - Function
Jelly Rolls - #830 / YefM-like fold - #60 / 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 ...Jelly Rolls - #830 / YefM-like fold - #60 / 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 / YefM-like fold / 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 / Metallopeptidase, catalytic domain superfamily / Neutral zinc metallopeptidases, zinc-binding region signature. / Jelly Rolls / Sandwich / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
beta-D-mannopyranose / A disintegrin and metalloproteinase with thrombospondin motifs 13
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsNakayama, D. / Akiyama, M. / Takeda, S. / Kokame, K. / Takagi, J. / Miyata, T.
Citation
Journal: To be Published
Title: Structural analysis and biochemical studies of ADAMTS13 P475S mutant
Authors: Nakayama, D. / Akiyama, M. / Takeda, S. / Kokame, K. / Takagi, J. / Miyata, T.
#1: Journal: Proc.Natl.Acad.Sci.USA / Year: 2009
Title: Crystal structures of the noncatalytic domains of ADAMTS13 reveal multiple discontinuous exosites for von Willebrand factor
Authors: Akiyama, M. / Takeda, S. / Kokame, K. / Takagi, J. / Miyata, T.
#2: Journal: J.Thromb.Haemost. / Year: 2008
Title: ADAMTS13 P475S polymorphism causes a lowered enzymatic activity and urea lability in vitro
Authors: Akiyama, M. / Kokame, K. / Miyata, T.
History
DepositionDec 21, 2011Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 26, 2012Provider: repository / Type: Initial release
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / 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_close_contact / struct_asym / struct_conn / struct_ref_seq_dif / 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 / _atom_site_anisotrop.pdbx_label_asym_id / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_validate_close_contact.auth_asym_id_1 / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_seq_id_1 / _pdbx_validate_close_contact.auth_seq_id_2 / _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 / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _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: A disintegrin and metalloproteinase with thrombospondin motifs 13
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,4915
Polymers45,3391
Non-polymers1,1524
Water81145
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: A disintegrin and metalloproteinase with thrombospondin motifs 13
hetero molecules

A: A disintegrin and metalloproteinase with thrombospondin motifs 13
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,98210
Polymers90,6782
Non-polymers2,3048
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area3110 Å2
ΔGint-10 kcal/mol
Surface area38800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)153.378, 53.243, 76.615
Angle α, β, γ (deg.)90.00, 111.56, 90.00
Int Tables number5
Space group name H-MC121

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Components

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Protein / Non-polymers , 2 types, 46 molecules A

#1: Protein 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: 45339.148 Da / Num. of mol.: 1 / Fragment: DTCS DOMAINS, UNP residues 287-685 / Mutation: P475S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ADAMTS13 / Plasmid: PCM-NIDSP / Cell line (production host): HEK293S Gnt1- / Production host: Cricetulus griseus (Chinese hamster) / References: UniProt: Q76LX8, ADAMTS13 endopeptidase
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 45 / Source method: isolated from a natural source / Formula: H2O

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Sugars , 4 types, 4 molecules

#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)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#3: Polysaccharide beta-D-glucopyranose-(1-3)-alpha-L-fucopyranose


Type: oligosaccharide / Mass: 326.297 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpb1-3LFucpa1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a1221m-1a_1-5][a2122h-1b_1-5]/1-2/a3-b1WURCSPDB2Glycan 1.1.0
[]{[(3+1)][a-L-Fucp]{[(3+1)][b-D-Glcp]{}}}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 / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1
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: Sugar ChemComp-BMA / beta-D-mannopyranose / beta-D-mannose / D-mannose / mannose / Mannose


Type: D-saccharide, beta linking / Mass: 180.156 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
IdentifierTypeProgram
DManpbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-mannopyranoseCOMMON NAMEGMML 1.0
b-D-ManpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
ManSNFG CARBOHYDRATE SYMBOLGMML 1.0

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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: 3.21 Å3/Da / Density % sol: 61.66 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 20% PEG1500, 0.1M MES, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL38B1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 21, 2011
RadiationMonochromator: Fixed exit Si (111) double crystal monochromator
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. all: 14407 / Num. obs: 14278 / % possible obs: 99.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Rmerge(I) obs: 0.048 / Net I/σ(I): 20.3
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.31 / Mean I/σ(I) obs: 6.28 / Num. unique all: 1405 / % possible all: 99

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Processing

Software
NameVersionClassification
HKL-2000data collection
MOLREPphasing
REFMAC5.5refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3GHM

3ghm


Resolution: 2.8→30.93 Å / Cor.coef. Fo:Fc: 0.926 / Cor.coef. Fo:Fc free: 0.899 / SU B: 30.293 / SU ML: 0.294 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R Free: 0.374 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.277 738 5.2 %RANDOM
Rwork0.229 ---
all0.232 13674 --
obs0.232 13509 98.79 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 62.369 Å2
Baniso -1Baniso -2Baniso -3
1--2.99 Å2-0 Å2-3.66 Å2
2--2.48 Å20 Å2
3----2.19 Å2
Refinement stepCycle: LAST / Resolution: 2.8→30.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2894 0 74 45 3013
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0213051
X-RAY DIFFRACTIONr_bond_other_d0.0010.022131
X-RAY DIFFRACTIONr_angle_refined_deg0.951.9784138
X-RAY DIFFRACTIONr_angle_other_deg0.73635108
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2375372
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.70322.158139
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.98515475
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.8821535
X-RAY DIFFRACTIONr_chiral_restr0.0550.2448
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0213385
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02652
X-RAY DIFFRACTIONr_mcbond_it0.3481.51860
X-RAY DIFFRACTIONr_mcbond_other0.0331.5762
X-RAY DIFFRACTIONr_mcangle_it0.66622984
X-RAY DIFFRACTIONr_scbond_it0.9531191
X-RAY DIFFRACTIONr_scangle_it1.6914.51154
LS refinement shellResolution: 2.8→2.87 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.354 48 -
Rwork0.283 929 -
obs-977 96.45 %
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)
11.7098-0.57622.3501-0.0636-0.16863.73110.1126-0.13610.15440.0008-0.0024-0.06520.2389-0.3072-0.11010.1091-0.0361-0.10610.39010.22910.21440.783733.5148-13.1102
21.8939-1.10381.44861.0224-1.68534.610.2118-0.3041-0.0954-0.2874-0.11940.04440.10740.0897-0.09240.25920.1003-0.10310.24020.02290.118433.811617.82410.7088
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A298 - 528
2X-RAY DIFFRACTION2A529 - 682

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