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- PDB-3edi: Crystal structure of tolloid-like protease 1 (TLL-1) protease domain -

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Basic information

Entry
Database: PDB / ID: 3edi
TitleCrystal structure of tolloid-like protease 1 (TLL-1) protease domain
ComponentsTolloid-like protein 1
KeywordsHYDROLASE / disordered cysteine-rich loop / Alternative splicing / Calcium / Developmental protein / Differentiation / EGF-like domain / Glycoprotein / Metal-binding / Metalloprotease / Polymorphism / Protease / Secreted / Zinc / Zymogen
Function / homology
Function and homology information


Anchoring fibril formation / Crosslinking of collagen fibrils / Collagen biosynthesis and modifying enzymes / dorsal/ventral pattern formation / Hydrolases; Acting on peptide bonds (peptidases); Metalloendopeptidases / collagen fibril organization / Degradation of the extracellular matrix / skeletal system development / protein processing / metalloendopeptidase activity ...Anchoring fibril formation / Crosslinking of collagen fibrils / Collagen biosynthesis and modifying enzymes / dorsal/ventral pattern formation / Hydrolases; Acting on peptide bonds (peptidases); Metalloendopeptidases / collagen fibril organization / Degradation of the extracellular matrix / skeletal system development / protein processing / metalloendopeptidase activity / cell differentiation / serine-type endopeptidase activity / calcium ion binding / extracellular space / zinc ion binding / extracellular region
Similarity search - Function
Bone morphogenetic protein 1/tolloid-like protein / Tolloid/BMP1 peptidase domain / : / Astacin-like domain profile. / Peptidase M12A / Astacin (Peptidase family M12A) / CUB domain / Domain first found in C1r, C1s, uEGF, and bone morphogenetic protein. / CUB domain / CUB domain profile. ...Bone morphogenetic protein 1/tolloid-like protein / Tolloid/BMP1 peptidase domain / : / Astacin-like domain profile. / Peptidase M12A / Astacin (Peptidase family M12A) / CUB domain / Domain first found in C1r, C1s, uEGF, and bone morphogenetic protein. / CUB domain / CUB domain profile. / Spermadhesin, CUB domain superfamily / Peptidase, metallopeptidase / Zinc-dependent metalloprotease / Collagenase (Catalytic Domain) / Collagenase (Catalytic Domain) / Coagulation Factor Xa inhibitory site / EGF-type aspartate/asparagine hydroxylation site / Metallopeptidase, catalytic domain superfamily / EGF-like calcium-binding, conserved site / Calcium-binding EGF-like domain signature. / EGF-like calcium-binding domain / Calcium-binding EGF-like domain / Epidermal growth factor-like domain. / EGF-like domain profile. / EGF-like domain signature 2. / EGF-like domain / Neutral zinc metallopeptidases, zinc-binding region signature. / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETYL GROUP / Tolloid-like protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.4 Å
AuthorsMac Sweeney, A.
CitationJournal: To be Published
Title: Structural basis for the substrate specificity of bone morphogenetic protein 1/tolloid-like metalloproteases
Authors: Mac Sweeney, A. / Parrado, S.G. / Vinzenz, D. / Bernardi, A. / Hein, A. / Bodendorf, U. / Erbel, P. / Logel, C. / Gerhartz, B.
History
DepositionSep 3, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 16, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Tolloid-like protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,5478
Polymers23,0061
Non-polymers5417
Water5,098283
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)41.281, 58.923, 47.444
Angle α, β, γ (deg.)90.000, 104.620, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Tolloid-like protein 1 / TLL-1


Mass: 23006.070 Da / Num. of mol.: 1 / Fragment: protease domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TLL1, TLL / Plasmid: pET24a / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta(DE3)
References: UniProt: O43897, Hydrolases; Acting on peptide bonds (peptidases); Metalloendopeptidases

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Non-polymers , 5 types, 290 molecules

#2: Chemical ChemComp-ACE / ACETYL GROUP


Mass: 44.053 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H4O
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 283 / Source method: isolated from a natural source / Formula: H2O

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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: 2.43 Å3/Da / Density % sol: 49.32 %
Crystal growTemperature: 277 K / Method: vapor diffusion / pH: 7.5
Details: 25% PEG 3350, 200mM lithium sulphate, 100mM Bis-Tris-HCl, pH 7.5, vapor diffusion, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.9999 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Oct 28, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9999 Å / Relative weight: 1
ReflectionResolution: 1.4→58.9 Å / Num. all: 43398 / Num. obs: 41793 / % possible obs: 96.3 % / Observed criterion σ(I): -3 / Redundancy: 3.5 % / Biso Wilson estimate: 20.8 Å2 / Rmerge(I) obs: 0.073 / Rsym value: 0.044 / Net I/σ(I): 15.9
Reflection shellResolution: 1.4→1.44 Å / Redundancy: 2.66 % / Rmerge(I) obs: 0.479 / Mean I/σ(I) obs: 2.9 / Num. unique all: 2592 / Rsym value: 0.327 / % possible all: 74.1

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å36.6 Å
Translation2.5 Å36.6 Å

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACT3.006data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1DLE

1dle


Resolution: 1.4→29.96 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.958 / WRfactor Rfree: 0.181 / WRfactor Rwork: 0.153 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.91 / SU B: 1.836 / SU ML: 0.033 / SU R Cruickshank DPI: 0.064 / SU Rfree: 0.057 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.064 / ESU R Free: 0.058 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.182 2090 5 %RANDOM
Rwork0.154 ---
obs0.155 41791 96.39 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 58.45 Å2 / Biso mean: 18.521 Å2 / Biso min: 5.51 Å2
Baniso -1Baniso -2Baniso -3
1--0.14 Å20 Å2-0.08 Å2
2--0.11 Å20 Å2
3----0.01 Å2
Refinement stepCycle: LAST / Resolution: 1.4→29.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1598 0 24 283 1905
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0211657
X-RAY DIFFRACTIONr_angle_refined_deg1.4731.9342242
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1355201
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.71622.18487
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.88715271
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.7971520
X-RAY DIFFRACTIONr_chiral_restr0.1030.2234
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.021284
X-RAY DIFFRACTIONr_nbd_refined0.2880.2819
X-RAY DIFFRACTIONr_nbtor_refined0.3120.21138
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2560.2211
X-RAY DIFFRACTIONr_metal_ion_refined0.0340.22
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3650.245
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.5910.226
X-RAY DIFFRACTIONr_mcbond_it1.8431.51010
X-RAY DIFFRACTIONr_mcangle_it2.74721592
X-RAY DIFFRACTIONr_scbond_it4.8733723
X-RAY DIFFRACTIONr_scangle_it5.074.5644
X-RAY DIFFRACTIONr_rigid_bond_restr4.47931733
X-RAY DIFFRACTIONr_sphericity_free7.683285
X-RAY DIFFRACTIONr_sphericity_bonded5.15831620
LS refinement shellResolution: 1.4→1.436 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.256 118 -
Rwork0.207 2237 -
all-2355 -
obs--73.69 %

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