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- PDB-2jih: Crystal Structure of Human ADAMTS-1 catalytic Domain and Cysteine... -

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Basic information

Entry
Database: PDB / ID: 2jih
TitleCrystal Structure of Human ADAMTS-1 catalytic Domain and Cysteine- Rich Domain (complex-form)
ComponentsADAMTS-1
KeywordsHYDROLASE / ZINC / ZYMOGEN / PROTEASE / ADAMTS-1 / METALLOPROTEASE / HEPARIN-BINDING / METALLOPROTEINASE / METZINCIN / POLYMORPHISM / GLYCOPROTEIN / METAL-BINDING / EXTRACELLULAR MATRIX / CLEAVAGE ON PAIR OF BASIC RESIDUES
Function / homology
Function and homology information


Defective B3GALTL causes PpS / O-glycosylation of TSR domain-containing proteins / ovulation from ovarian follicle / heart trabecula formation / Hydrolases; Acting on peptide bonds (peptidases); Metalloendopeptidases / positive regulation of vascular associated smooth muscle cell migration / basement membrane / positive regulation of G1/S transition of mitotic cell cycle / positive regulation of vascular associated smooth muscle cell proliferation / Degradation of the extracellular matrix ...Defective B3GALTL causes PpS / O-glycosylation of TSR domain-containing proteins / ovulation from ovarian follicle / heart trabecula formation / Hydrolases; Acting on peptide bonds (peptidases); Metalloendopeptidases / positive regulation of vascular associated smooth muscle cell migration / basement membrane / positive regulation of G1/S transition of mitotic cell cycle / positive regulation of vascular associated smooth muscle cell proliferation / Degradation of the extracellular matrix / extracellular matrix organization / negative regulation of angiogenesis / extracellular matrix / kidney development / integrin-mediated signaling pathway / metalloendopeptidase activity / metallopeptidase activity / heparin binding / cytoplasmic vesicle / negative regulation of cell population proliferation / proteolysis / zinc ion binding / extracellular region
Similarity search - Function
Peptidase M12B, ADAM-TS1 / 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 ...Peptidase M12B, ADAM-TS1 / 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 / Peptidase M12B, propeptide / Reprolysin family propeptide / Reprolysin (M12B) family zinc metalloprotease / Peptidase M12B, ADAM/reprolysin / ADAM type metalloprotease domain profile. / 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 / Collagenase (Catalytic Domain) / Collagenase (Catalytic Domain) / Metallopeptidase, catalytic domain superfamily / Neutral zinc metallopeptidases, zinc-binding region signature. / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-097 / : / NICKEL (II) ION / A disintegrin and metalloproteinase with thrombospondin motifs 1
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsGerhardt, S. / Hassall, G. / Hawtin, P. / McCall, E. / Flavell, L. / Minshull, C. / Hargreaves, D. / Ting, A. / Pauptit, R.A. / Parker, A.E. / Abbott, W.M.
CitationJournal: J. Mol. Biol. / Year: 2007
Title: Crystal structures of human ADAMTS-1 reveal a conserved catalytic domain and a disintegrin-like domain with a fold homologous to cysteine-rich domains.
Authors: Gerhardt, S. / Hassall, G. / Hawtin, P. / McCall, E. / Flavell, L. / Minshull, C. / Hargreaves, D. / Ting, A. / Pauptit, R.A. / Parker, A.E. / Abbott, W.M.
History
DepositionJun 28, 2007Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 15, 2008Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 28, 2018Group: Database references / Source and taxonomy / Category: citation / citation_author / entity_src_gen
Item: _citation.journal_abbrev / _citation.page_last ..._citation.journal_abbrev / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _citation_author.name / _entity_src_gen.pdbx_host_org_cell_line / _entity_src_gen.pdbx_host_org_strain
Revision 1.4Apr 24, 2019Group: Data collection / Source and taxonomy / Category: entity_src_gen / Item: _entity_src_gen.pdbx_host_org_cell_line

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ADAMTS-1
B: ADAMTS-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,25735
Polymers65,8242
Non-polymers2,43333
Water3,783210
1
A: ADAMTS-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,28719
Polymers32,9121
Non-polymers1,37518
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: ADAMTS-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,97016
Polymers32,9121
Non-polymers1,05815
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)51.579, 64.396, 113.524
Angle α, β, γ (deg.)90.00, 90.91, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein ADAMTS-1 / / A DISINTEGRIN AND METALLOPROTEINASE WITH THROMBOSPONDIN MOTIFS 1 / ADAM-TS 1 / ADAM-TS1 / METH-1


Mass: 32911.938 Da / Num. of mol.: 2
Fragment: CATALYTIC DOMAIN AND CYSTEINE-RICH DOMAIN, RESIDUES 253-548
Source method: isolated from a genetically manipulated source
Details: MARIMASTAT (N4-(2,2-DIMETHYL-1-METHYLCARBAMOYL-PROPYL)-2, N1-DIHYDROXY-3-ISOBUTYL-SUCCINAMIDE)
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PFASTBAC / Cell line (production host): Sf21 / Production host: SPODOPTERA FRUGIPERDA (fall armyworm) / References: UniProt: Q9UHI8

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Non-polymers , 7 types, 243 molecules

#2: Chemical ChemComp-097 / (2S,3R)-N~4~-[(1S)-2,2-dimethyl-1-(methylcarbamoyl)propyl]-N~1~,2-dihydroxy-3-(2-methylpropyl)butanediamide / MARIMASTAT / Marimastat


Mass: 331.408 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H29N3O5 / Comment: antineoplastic, inhibitor*YM
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#4: Chemical
ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Cd
#5: Chemical
ChemComp-NI / NICKEL (II) ION / Nickel


Mass: 58.693 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Ni
#6: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Mg
#7: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Na
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 210 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsSWISSPROT ENTRY Q9UHI8

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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: 2.88 Å3/Da / Density % sol: 57 % / Description: NONE
Crystal growpH: 7
Details: 0.2-0.6M SODIUM ACETATE, 0.05M CADMIUM SULPHATE, 0.1M HEPES PH 7.0, 12-22% GLYCEROL

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418
DetectorType: RIGAKU CCD / Detector: CCD / Date: Jun 14, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.1→56.9 Å / Num. obs: 35439 / % possible obs: 99.9 % / Observed criterion σ(I): 2 / Redundancy: 3 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 9
Reflection shellResolution: 2.1→2.18 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.25 / Mean I/σ(I) obs: 2 / % possible all: 70.6

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Processing

Software
NameVersionClassification
REFMAC5.2refinement
d*TREKdata reduction
d*TREKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→56.9 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.891 / SU B: 15.993 / SU ML: 0.186 / Cross valid method: THROUGHOUT / ESU R: 0.285 / ESU R Free: 0.24 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.282 1792 5.1 %RANDOM
Rwork0.224 ---
obs0.227 33647 82.6 %-
Displacement parametersBiso mean: 35.5 Å2
Refinement stepCycle: LAST / Resolution: 2.1→56.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4380 0 77 210 4667
LS refinement shellResolution: 2.1→2.15 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.31 119
Rwork0.264 2050

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