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- PDB-1cqr: CRYSTAL STRUCTURE OF THE STROMELYSIN CATALYTIC DOMAIN AT 2.0 A RE... -

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Basic information

Entry
Database: PDB / ID: 1cqr
TitleCRYSTAL STRUCTURE OF THE STROMELYSIN CATALYTIC DOMAIN AT 2.0 A RESOLUTION
ComponentsSTROMELYSIN-1Matrix metalloproteinase
KeywordsHYDROLASE / ACTIVE / TRUNCATED NATIVE ENZYME
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 / EGFR Transactivation by Gastrin / extracellular matrix / Degradation of the extracellular matrix / extracellular matrix organization / positive regulation of protein-containing complex assembly / metalloendopeptidase activity / cellular response to reactive oxygen species / metallopeptidase activity / peptidase activity / Interleukin-4 and Interleukin-13 signaling / endopeptidase activity / cellular response to lipopolysaccharide / Extra-nuclear estrogen signaling / serine-type endopeptidase activity / innate immune response / proteolysis / extracellular space / zinc ion binding / extracellular region / nucleus / cytoplasm
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
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / Resolution: 2 Å
AuthorsChen, L. / Rydel, T.J. / Gu, F. / Dunaway, C.M. / Pikul, S. / Dunham, K.M. / Barnett, B.L.
Citation
Journal: J.Mol.Biol. / Year: 1999
Title: Crystal structure of the stromelysin catalytic domain at 2.0 A resolution: inhibitor-induced conformational changes.
Authors: Chen, L. / Rydel, T.J. / Gu, F. / Dunaway, C.M. / Pikul, S. / Dunham, K.M. / Barnett, B.L.
#1: Journal: J.Med.Chem. / Year: 1999
Title: Design and Synthesis of Phosphinamide-Based Hydroxamic Acids as Inhibitors of Matrix Metalloproteinases
Authors: Pikul, S. / McDow Dunham, K.L. / Almstead, N.G. / De, B. / Natchus, M.G. / Anastasio, M.V. / McPhail, S.J. / Snider, C.E. / Taiwo, Y.O. / Chen, L. / Dunaway, C.M. / Gu, F. / Mieling, G.E.
History
DepositionAug 11, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 20, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / 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_asym_id / _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_asym_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_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_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)39,33512
Polymers38,8332
Non-polymers50210
Water1,47782
1
A: STROMELYSIN-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,6686
Polymers19,4171
Non-polymers2515
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: STROMELYSIN-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,6686
Polymers19,4171
Non-polymers2515
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
A: STROMELYSIN-1
hetero molecules

B: STROMELYSIN-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,33512
Polymers38,8332
Non-polymers50210
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_464-x-1/2,-y+1,z-1/21
Buried area1660 Å2
ΔGint-130 kcal/mol
Surface area16580 Å2
MethodPISA, PQS
4


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)38.2, 79.1, 107.4
Angle α, β, γ (deg.)90., 90., 90.
Int Tables number19
Cell settingorthorhombic
Space group name H-MP212121
DetailsThe biological assembly is a monomer

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Components

#1: Protein STROMELYSIN-1 / Matrix metalloproteinase / E.C.3.4.24.17 / HUMAN MATRIX METALLOPROTEINASE-3


Mass: 19416.529 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: P08254, stromelysin 1
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 82 / 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: 2.09 Å3/Da / Density % sol: 41.08 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 20-24% PEG 8000, 2.5% 2-propanol, 10mM CaCl2, 0.1 M Tris-HCL buffer, VAPOR DIFFUSION, HANGING DROP, temperature 298.K
Crystal grow
*PLUS
Method: vapor diffusion / PH range low: 8.5 / PH range high: 7.5
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
110 mg/mlprotein1drop
220-24 %(w/v)PEG80001reservoir
32.5 %(v/v)2-propanol1reservoir
410 mM1reservoirCaCl2
50.1 MTris-HCl1reservoir

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS II / Detector: IMAGE PLATE / Date: May 24, 1996
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→12 Å / Num. all: 24377 / Num. obs: 21471 / % possible obs: 94.7 % / Observed criterion σ(F): 2 / Redundancy: 4.3 % / Biso Wilson estimate: 12.7 Å2 / Rmerge(I) obs: 0.058 / Net I/σ(I): 10.9
Reflection shellResolution: 2→12 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.058 / Num. unique all: 24377 / % possible all: 94.7
Reflection shell
*PLUS
% possible obs: 94.7 %

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Processing

Software
NameVersionClassification
AMoREphasing
X-PLOR3.1refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementResolution: 2→12 Å / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 1 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.266 2147 10 %Random
Rwork0.199 ---
all0.266 24377 --
obs0.199 21471 90.1 %-
Refinement stepCycle: LAST / Resolution: 2→12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2722 0 10 82 2814
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.017
X-RAY DIFFRACTIONx_angle_deg3.21

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