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- PDB-2usn: CRYSTAL STRUCTURE OF THE CATALYTIC DOMAIN OF HUMAN FIBROBLAST STR... -

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Basic information

Entry
Database: PDB / ID: 2usn
TitleCRYSTAL STRUCTURE OF THE CATALYTIC DOMAIN OF HUMAN FIBROBLAST STROMELYSIN-1 INHIBITED WITH THIADIAZOLE INHIBITOR PNU-141803
ComponentsSTROMELYSIN-1
KeywordsHYDROLASE / METALLOPROTEASE / FIBROBLAST / COLLAGEN DEGRADATION
Function / homology
Function and homology information


stromelysin 1 / cellular response to UV-A / regulation of neuroinflammatory response / Assembly of collagen fibrils and other multimeric structures / Activation of Matrix Metalloproteinases / response to amyloid-beta / Collagen degradation / collagen catabolic process / extracellular matrix disassembly / cellular response to nitric oxide ...stromelysin 1 / cellular response to UV-A / regulation of neuroinflammatory response / Assembly of collagen fibrils and other multimeric structures / Activation of Matrix Metalloproteinases / response to amyloid-beta / Collagen degradation / collagen catabolic process / extracellular matrix disassembly / cellular response to nitric oxide / negative regulation of reactive oxygen species metabolic process / negative regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / regulation of cell migration / EGFR Transactivation by Gastrin / Degradation of the extracellular matrix / extracellular matrix organization / extracellular matrix / cellular response to amino acid stimulus / protein catabolic process / positive regulation of protein-containing complex assembly / metalloendopeptidase activity / cellular response to reactive oxygen species / metallopeptidase activity / peptidase activity / cellular response to lipopolysaccharide / Interleukin-4 and Interleukin-13 signaling / endopeptidase activity / Extra-nuclear estrogen signaling / serine-type endopeptidase activity / innate immune response / mitochondrion / proteolysis / extracellular space / zinc ion binding / extracellular region / nucleus / cytosol
Similarity search - Function
Peptidoglycan binding-like / Hemopexin, conserved site / Hemopexin domain signature. / Hemopexin-like domain / Peptidase M10A, cysteine switch, zinc binding site / Matrixins cysteine switch. / Putative peptidoglycan binding domain / Hemopexin-like repeats / Hemopexin-like domain superfamily / Hemopexin ...Peptidoglycan binding-like / Hemopexin, conserved site / Hemopexin domain signature. / Hemopexin-like domain / Peptidase M10A, cysteine switch, zinc binding site / Matrixins cysteine switch. / Putative peptidoglycan binding domain / Hemopexin-like repeats / Hemopexin-like domain superfamily / Hemopexin / Hemopexin repeat profile. / Hemopexin-like repeats. / Peptidase M10A / Peptidase M10A, catalytic domain / Peptidase M10, metallopeptidase / Matrixin / PGBD-like superfamily / Peptidase, metallopeptidase / Zinc-dependent metalloprotease / 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-IN8 / Stromelysin-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsFinzel, B.C. / Bryant Junior, G.L. / Baldwin, E.T.
CitationJournal: Protein Sci. / Year: 1998
Title: Structural characterizations of nonpeptidic thiadiazole inhibitors of matrix metalloproteinases reveal the basis for stromelysin selectivity.
Authors: Finzel, B.C. / Baldwin, E.T. / Bryant Jr., G.L. / Hess, G.F. / Wilks, J.W. / Trepod, C.M. / Mott, J.E. / Marshall, V.P. / Petzold, G.L. / Poorman, R.A. / O'Sullivan, T.J. / Schostarez, H.J. / Mitchell, M.A.
History
DepositionJun 9, 1998Processing site: BNL
Revision 1.0Dec 23, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 25, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 7, 2018Group: Data collection / Other / Category: diffrn_source / pdbx_database_status
Item: _diffrn_source.source / _pdbx_database_status.process_site
Revision 1.4Aug 9, 2023Group: Database references / Derived calculations / Refinement description
Category: database_2 / pdbx_initial_refinement_model ...database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / pdbx_struct_special_symmetry / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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.ptnr1_symmetry / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: STROMELYSIN-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,3278
Polymers18,5961
Non-polymers7317
Water1,51384
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)70.890, 70.890, 189.110
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11A-262-

ZN

21A-263-

HOH

31A-359-

HOH

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Components

#1: Protein STROMELYSIN-1 / MATRIX METALLOPROTEINASE-3 / PROTEOGLYCANASE


Mass: 18595.684 Da / Num. of mol.: 1 / Fragment: CATALYTIC DOMAIN RESIDUES 83 - 247
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell: FIBROBLAST / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P08254, stromelysin 1
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-IN8 / [2-(5-MERCAPTO-[1,3,4]THIADIAZOL-2-YLCARBAMOYL)-1-PHENYL-ETHYL]-CARBAMIC ACID BENZYL ESTER / PNU-141803


Mass: 414.501 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H18N4O3S2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 84 / 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: 2.46 Å3/Da / Density % sol: 49.95 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 7
Details: HANGING DROP VAPOR DIFFUSION., pH 7.0, vapor diffusion - hanging drop
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop / Details: inhibitor solution : protein = 1:10
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
110 mMinhibitor1drop
2100 %DMSO1dropin inhibitor solution
313 mg/mlprotein1drop
422.5 %PEG60001reservoir

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: ROTATING ANODE / Type: SIEMENS / Wavelength: 1.5418
DetectorType: SIEMENS / Detector: AREA DETECTOR / Date: Apr 29, 1996
RadiationMonochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.2→20 Å / Num. obs: 8566 / % possible obs: 88 % / Observed criterion σ(I): 1 / Redundancy: 4.52 % / Rsym value: 0.086 / Net I/σ(I): 8
Reflection shellResolution: 2.2→2.33 Å / Mean I/σ(I) obs: 4.3 / Rsym value: 0.192 / % possible all: 77
Reflection
*PLUS
Num. measured all: 38781 / Rmerge(I) obs: 0.086
Reflection shell
*PLUS
% possible obs: 77 % / Rmerge(I) obs: 0.192

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Processing

Software
NameClassification
X-PLORmodel building
PROFFTrefinement
X-PLORrefinement
XENGENdata reduction
XENGENdata scaling
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PROTEIN COMPONENT OF STROMELYSIN-1 MODEL WITH OTHER INHIBITOR (1USN)

1usn


Resolution: 2.2→10 Å / σ(F): 2
Details: SEILECKI ET AL (JMB V134, 1979) PARAMETERS USED IN REFINEMENT. THROUGHOUT THE MODEL, RESIDUES ARE NUMBERED RELATIVE TO THE SEQUENCE OF THE PROENZYME. THE FIRST RESIDUE OF THE MATURE ACTIVE ...Details: SEILECKI ET AL (JMB V134, 1979) PARAMETERS USED IN REFINEMENT. THROUGHOUT THE MODEL, RESIDUES ARE NUMBERED RELATIVE TO THE SEQUENCE OF THE PROENZYME. THE FIRST RESIDUE OF THE MATURE ACTIVE CATALYTIC DOMAIN IS PHE 83. RESIDUES 190-191 ARE PARTIALY DISORDERED. THE CONFORMATION OF THESE ATOMS IS UNCERTAIN. SIDECHAINS OF RESIDUES ASP 111 AND GLU 216 ARE MODELED IN TWO DISCRETE CONFORMATIONS. THE MODEL INCLUDES A CATALYTIC ZN+2 (257), A STRUCTURAL ZN+2 (258), AND THREE BOUND CA+2 IONS (259-261). A THIRD ZN+2 HAS BEEN IDENTIFIED IN THIS CRYSTAL FORM AND RESTS ON THE CRYSTALLOGRAPHIC THREE-FOLD AXIS, COORDINATED BY THREE CRYSTALLOGRAPHICALLY RELATED OCCURANCES OF HIS 96 NE2 AND AN UNKNOWN FOURTH LIGAND. THE FOURTH LIGAND IS MODELED WITH TWO ATOMS. ONE (HOH 263 O) COORDINATED TO THE ZN 262 ALSO SITS ON THE THREE-FOLD AXIS. ONE ATOM (HOH 264 O) BONDED (2.05 ANGSTROMS) TO IT. THIS SECOND ATOM IS REPLICATED THREE TIMES BY SYMMETRY. THE FOURTH LIGAND THEREFORE RESEMBLES A CARBONATE OR NITRITE ION.
RfactorNum. reflection% reflection
Rwork0.172 --
obs0.172 8429 82 %
Displacement parametersBiso mean: 19.11 Å2
Refinement stepCycle: LAST / Resolution: 2.2→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1312 0 34 84 1430
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0150.02
X-RAY DIFFRACTIONp_angle_d0.0320.03
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0350.04
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it0.7481
X-RAY DIFFRACTIONp_mcangle_it1.2552
X-RAY DIFFRACTIONp_scbond_it1.331.5
X-RAY DIFFRACTIONp_scangle_it1.9983
X-RAY DIFFRACTIONp_plane_restr0.0220.03
X-RAY DIFFRACTIONp_chiral_restr0.2540.25
X-RAY DIFFRACTIONp_singtor_nbd0.180.4
X-RAY DIFFRACTIONp_multtor_nbd0.2070.4
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd0.250.4
X-RAY DIFFRACTIONp_planar_tor3.23
X-RAY DIFFRACTIONp_staggered_tor10.15
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor21.710
X-RAY DIFFRACTIONp_special_tor
Software
*PLUS
Name: PROFFT / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
LS refinement shell
*PLUS
Highest resolution: 2.2 Å / Lowest resolution: 2.3 Å

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