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- PDB-1usn: CRYSTAL STRUCTURE OF THE CATALYTIC DOMAIN OF HUMAN FIBROBLAST STR... -

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Entry
Database: PDB / ID: 1usn
TitleCRYSTAL STRUCTURE OF THE CATALYTIC DOMAIN OF HUMAN FIBROBLAST STROMELYSIN-1 INHIBITED WITH THIADIAZOLE INHIBITOR PNU-142372
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-IN9 / Stromelysin-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.8 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 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Nov 29, 2017Group: Derived calculations / Other
Category: pdbx_database_status / struct_conf / struct_conf_type
Item: _pdbx_database_status.process_site
Revision 1.4Mar 7, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.source
Revision 1.5Aug 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 1.6May 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)19,3408
Polymers18,5961
Non-polymers7447
Water2,000111
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: STROMELYSIN-1
hetero molecules

A: STROMELYSIN-1
hetero molecules

A: STROMELYSIN-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,01924
Polymers55,7873
Non-polymers2,23221
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-y+1,x-y,z1
crystal symmetry operation3_665-x+y+1,-x+1,z1
Buried area4030 Å2
ΔGint-260 kcal/mol
Surface area24820 Å2
MethodPISA
3
A: STROMELYSIN-1
hetero molecules

A: STROMELYSIN-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,67916
Polymers37,1912
Non-polymers1,48814
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation11_565x-y+2/3,-y+4/3,-z+1/31
MethodPQS
Unit cell
Length a, b, c (Å)72.120, 72.120, 192.060
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-IN9 / 2-[3-(5-MERCAPTO-[1,3,4]THIADIAZOL-2YL)-UREIDO]-N-METHYL-3-PENTAFLUOROPHENYL-PROPIONAMIDE / PNU-142372


Mass: 427.373 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C13H10F5N5O2S2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 111 / 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: 2.58 Å3/Da / Density % sol: 52.38 %
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
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
114.8 mg/mlenzyme1drop
210 mMHEPES1drop
35 mM1dropCaCl2
42 mM1dropZnCl2
50.02 %1dropNaN3
625 mg/mlPNU-1423721drop
7100 %PEG4001drop
80.1 M1reservoirLiSO4
90.1 MHEPES1reservoir
1020-25 %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: Nov 15, 1995
RadiationMonochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.6→20 Å / Num. obs: 20522 / % possible obs: 95 % / Observed criterion σ(I): 1 / Redundancy: 4.69 % / Rsym value: 0.075 / Net I/σ(I): 10.4
Reflection shellResolution: 1.61→1.71 Å / Mean I/σ(I) obs: 1.83 / Rsym value: 0.239 / % possible all: 49
Reflection
*PLUS
Num. measured all: 96250 / Rmerge(I) obs: 0.075
Reflection shell
*PLUS
% possible obs: 49 % / Rmerge(I) obs: 0.239

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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 (J. W. BECKER, ET AL.; 1SLN)

1sln


Resolution: 1.8→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, ASN 214 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 ZN 262 ALSO SITS ON THE THREE-FOLD AXIS AND 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
Rwork0.189 --
obs0.189 17046 95 %
Displacement parametersBiso mean: 19.11 Å2
Refinement stepCycle: LAST / Resolution: 1.8→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1312 0 33 111 1456
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0180.02
X-RAY DIFFRACTIONp_angle_d0.040.03
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.050.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it0.8351
X-RAY DIFFRACTIONp_mcangle_it1.3522
X-RAY DIFFRACTIONp_scbond_it1.6811.5
X-RAY DIFFRACTIONp_scangle_it2.4763
X-RAY DIFFRACTIONp_plane_restr0.0260.03
X-RAY DIFFRACTIONp_chiral_restr0.2750.25
X-RAY DIFFRACTIONp_singtor_nbd0.1670.4
X-RAY DIFFRACTIONp_multtor_nbd0.1730.4
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd0.2090.4
X-RAY DIFFRACTIONp_planar_tor3.83
X-RAY DIFFRACTIONp_staggered_tor10.35
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor24.110
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: 1.8 Å / Lowest resolution: 1.9 Å

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