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- PDB-1hv5: CRYSTAL STRUCTURE OF THE STROMELYSIN-3 (MMP-11) CATALYTIC DOMAIN ... -

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Basic information

Entry
Database: PDB / ID: 1hv5
TitleCRYSTAL STRUCTURE OF THE STROMELYSIN-3 (MMP-11) CATALYTIC DOMAIN COMPLEXED WITH A PHOSPHINIC INHIBITOR
ComponentsSTROMELYSIN 3
KeywordsHYDROLASE / stromelysin-3 / inhibition / phosphinic inhibitor
Function / homology
Function and homology information


Activation of Matrix Metalloproteinases / Collagen degradation / Degradation of the extracellular matrix / basement membrane organization / Hydrolases; Acting on peptide bonds (peptidases); Metalloendopeptidases / collagen fibril organization / negative regulation of fat cell differentiation / collagen catabolic process / extracellular matrix organization / extracellular matrix ...Activation of Matrix Metalloproteinases / Collagen degradation / Degradation of the extracellular matrix / basement membrane organization / Hydrolases; Acting on peptide bonds (peptidases); Metalloendopeptidases / collagen fibril organization / negative regulation of fat cell differentiation / collagen catabolic process / extracellular matrix organization / extracellular matrix / metalloendopeptidase activity / metallopeptidase activity / proteolysis / extracellular region / zinc ion binding
Similarity search - Function
Hemopexin, conserved site / Hemopexin domain signature. / Hemopexin-like domain / Hemopexin-like repeats / Hemopexin-like domain superfamily / Hemopexin / Hemopexin repeat profile. / Hemopexin-like repeats. / Peptidase M10A / Peptidase M10A, catalytic domain ...Hemopexin, conserved site / Hemopexin domain signature. / Hemopexin-like 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 / 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-RXP / Stromelysin-3
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsGall, A.L. / Ruff, M. / Kannan, R. / Cuniasse, P. / Yiotakis, A. / Dive, V. / Rio, M.C. / Basset, P. / Moras, D.
CitationJournal: J.Mol.Biol. / Year: 2001
Title: Crystal structure of the stromelysin-3 (MMP-11) catalytic domain complexed with a phosphinic inhibitor mimicking the transition-state.
Authors: Gall, A.L. / Ruff, M. / Kannan, R. / Cuniasse, P. / Yiotakis, A. / Dive, V. / Rio, M.C. / Basset, P. / Moras, D.
History
DepositionJan 8, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 28, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: 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_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.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.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.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_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 3
B: STROMELYSIN 3
C: STROMELYSIN 3
D: STROMELYSIN 3
E: STROMELYSIN 3
F: STROMELYSIN 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)126,97742
Polymers114,4046
Non-polymers12,57236
Water38,4802136
1
A: STROMELYSIN 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,1637
Polymers19,0671
Non-polymers2,0956
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: STROMELYSIN 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,1637
Polymers19,0671
Non-polymers2,0956
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: STROMELYSIN 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,1637
Polymers19,0671
Non-polymers2,0956
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: STROMELYSIN 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,1637
Polymers19,0671
Non-polymers2,0956
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: STROMELYSIN 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,1637
Polymers19,0671
Non-polymers2,0956
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: STROMELYSIN 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,1637
Polymers19,0671
Non-polymers2,0956
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)140.100, 148.500, 91.400
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Cell settingorthorhombic
Space group name H-MP212121

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Components

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Protein , 1 types, 6 molecules ABCDEF

#1: Protein
STROMELYSIN 3 / E.C.3.4.24.- / MATRIX METALLOPROTEINASE 11 / MMP-11 / ST3 / SL-3


Mass: 19067.387 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: STRO3 (101-264) / Plasmid: PET 3B / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21
References: UniProt: Q02853, Hydrolases; Acting on peptide bonds (peptidases); Metalloendopeptidases

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Non-polymers , 5 types, 2172 molecules

#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 12 / 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: Chemical
ChemComp-CPS / 3-[(3-CHOLAMIDOPROPYL)DIMETHYLAMMONIO]-1-PROPANESULFONATE / CHAPS


Mass: 614.877 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C32H58N2O7S / Comment: detergent*YM
#5: Chemical
ChemComp-RXP / 1-BENZYLOXYCARBONYLAMINO-2-PHENYL-ETHYL)-{2-[1-CARBAMOYL-2-(1H-INDOL-3-YL)-ETHYLCARBAMOYL]-5-PHENYL-PENTYL}-PHOSPHINIC ACID


Mass: 694.756 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C39H43N4O6P
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2136 / 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: 4.15 Å3/Da / Density % sol: 70.39 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: Ammonium sulfate, CHAPS, VAPOR DIFFUSION, HANGING DROP at pH 5.5 at 277K
Crystal grow
*PLUS
Temperature: 4 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
15 mg/mlprotein1drop
20.25 mMphosphinic inhibitor RXP031drop
350 mMMES1drop
4500 mMammonium sulfate1drop
550 mMMES1reservoir
6500 mMammonium sulfate1reservoir
71 %(v/v)trifluoroethanol1reservoir

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Data collection

DiffractionMean temperature: 220 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.98 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.6→20 Å / Num. obs: 57370 / % possible obs: 100 % / Biso Wilson estimate: 16.8 Å2 / Net I/σ(I): 19.96
Reflection
*PLUS
Rmerge(I) obs: 0.119

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Processing

Software
NameVersionClassification
DENZOdata reduction
XDSdata reduction
AMoREphasing
CNS1refinement
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.6→19.89 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 2225596.64 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.262 5828 10.2 %RANDOM
Rwork0.218 ---
obs0.218 57370 96.9 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 32.01 Å2 / ksol: 0.309 e/Å3
Displacement parametersBiso mean: 35.7 Å2
Baniso -1Baniso -2Baniso -3
1--7.5 Å20 Å20 Å2
2--7.28 Å20 Å2
3---0.22 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.36 Å0.29 Å
Luzzati d res low-5 Å
Luzzati sigma a0.38 Å0.31 Å
Refinement stepCycle: LAST / Resolution: 2.6→19.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7990 0 646 2136 10772
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.018
X-RAY DIFFRACTIONc_angle_deg2.2
X-RAY DIFFRACTIONc_dihedral_angle_d24.1
X-RAY DIFFRACTIONc_improper_angle_d1.57
X-RAY DIFFRACTIONc_mcbond_it1.011.5
X-RAY DIFFRACTIONc_mcangle_it1.782
X-RAY DIFFRACTIONc_scbond_it1.362
X-RAY DIFFRACTIONc_scangle_it2.172.5
LS refinement shellResolution: 2.6→2.76 Å / Rfactor Rfree error: 0.01 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.309 883 9.8 %
Rwork0.263 8098 -
obs--92.3 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PAPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAWATER.TOP
X-RAY DIFFRACTION3CHAPS_ALL.PARCHAPS_ALL.TOP
X-RAY DIFFRACTION4RXPO3.PARRXPO3.TOP
X-RAY DIFFRACTION5ION.PARAMION.TOP
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg24.1
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.57

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