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- PDB-5lab: Crystal structure of the catalytic domain of human MMP12 complexe... -

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Basic information

Entry
Database: PDB / ID: 5lab
TitleCrystal structure of the catalytic domain of human MMP12 complexed with the inhibitor NNGH
ComponentsMacrophage metalloelastase
KeywordsHYDROLASE / HYDROLASE MMP-12
Function / homology
Function and homology information


macrophage elastase / negative regulation of endothelial cell-matrix adhesion via fibronectin / bronchiole development / positive regulation of epithelial cell proliferation involved in wound healing / elastin catabolic process / regulation of defense response to virus by host / positive regulation of type I interferon-mediated signaling pathway / wound healing, spreading of epidermal cells / negative regulation of type I interferon-mediated signaling pathway / lung alveolus development ...macrophage elastase / negative regulation of endothelial cell-matrix adhesion via fibronectin / bronchiole development / positive regulation of epithelial cell proliferation involved in wound healing / elastin catabolic process / regulation of defense response to virus by host / positive regulation of type I interferon-mediated signaling pathway / wound healing, spreading of epidermal cells / negative regulation of type I interferon-mediated signaling pathway / lung alveolus development / response to amyloid-beta / positive regulation of interferon-alpha production / Collagen degradation / collagen catabolic process / extracellular matrix disassembly / core promoter sequence-specific DNA binding / collagen binding / Degradation of the extracellular matrix / extracellular matrix organization / extracellular matrix / metalloendopeptidase activity / cellular response to virus / protein import into nucleus / endopeptidase activity / sequence-specific DNA binding / serine-type endopeptidase activity / calcium ion binding / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / proteolysis / extracellular space / zinc ion binding / extracellular region / nucleus / cytoplasm
Similarity search - Function
Hemopexin, conserved site / Hemopexin domain signature. / Hemopexin-like domain / Peptidoglycan binding-like / Peptidase M10A, cysteine switch, zinc binding site / Matrixins cysteine switch. / Hemopexin-like repeats / Hemopexin-like domain superfamily / Hemopexin / Putative peptidoglycan binding domain ...Hemopexin, conserved site / Hemopexin domain signature. / Hemopexin-like domain / Peptidoglycan binding-like / Peptidase M10A, cysteine switch, zinc binding site / Matrixins cysteine switch. / Hemopexin-like repeats / Hemopexin-like domain superfamily / Hemopexin / Putative peptidoglycan binding domain / 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-NGH / Macrophage metalloelastase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.34 Å
AuthorsRavera, E. / Calderone, V. / Luchinat, C.
Citation
Journal: To Be Published
Title: First-principles calculation of pseudo-contact shifts in a paramagnetic metalloprotein
Authors: Benda, L. / Mares, J. / Ravera, E. / Parigi, G. / Luchinat, C. / Kaupp, M. / Vaara, J.
#1: Journal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2005
Title: Conformational variability of matrix metalloproteinases: beyond a single 3D structure.
Authors: Bertini, I. / Calderone, V. / Cosenza, M. / Fragai, M. / Lee, Y.M. / Luchinat, C. / Mangani, S. / Terni, B. / Turano, P.
History
DepositionJun 14, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 10, 2016Provider: repository / Type: Initial release
Revision 1.1Feb 7, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Jan 29, 2025Group: Advisory / Structure summary / Category: pdbx_database_PDB_obs_spr / pdbx_entry_details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Macrophage metalloelastase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,1837
Polymers17,6161
Non-polymers5676
Water4,252236
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area930 Å2
ΔGint-63 kcal/mol
Surface area7990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.190, 62.560, 37.260
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-626-

HOH

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Components

#1: Protein Macrophage metalloelastase / MME / Macrophage elastase / hME / Matrix metalloproteinase-12 / MMP-12


Mass: 17615.670 Da / Num. of mol.: 1 / Fragment: UNP residues 106-263 / Mutation: F171D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MMP12, HME / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P39900, macrophage elastase
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / 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-NGH / N-ISOBUTYL-N-[4-METHOXYPHENYLSULFONYL]GLYCYL HYDROXAMIC ACID


Mass: 316.373 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C13H20N2O5S
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 236 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

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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: 2.26 Å3/Da / Density % sol: 45.26 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8
Details: Tris, PEG6000, NNGH, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 5.2R / Wavelength: 1.2 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Oct 5, 2003
RadiationMonochromator: double-crystal monochromator Si(111) and Si(220)
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.2 Å / Relative weight: 1
ReflectionResolution: 1.34→46.407 Å / Num. obs: 36295 / % possible obs: 98.4 % / Redundancy: 6.2 % / Net I/σ(I): 7.2
Reflection shellResolution: 1.34→1.41 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.308 / Mean I/σ(I) obs: 2.3 / % possible all: 92.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0103refinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1OS9

1os9


Resolution: 1.34→20 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.963 / SU B: 2.615 / SU ML: 0.046 / Cross valid method: THROUGHOUT / ESU R: 0.059 / ESU R Free: 0.057 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.1945 2575 7.1 %RANDOM
Rwork0.15515 ---
obs0.15789 33671 98.5 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 21.754 Å2
Baniso -1Baniso -2Baniso -3
1--1.5 Å2-0 Å2-0 Å2
2---0.52 Å20 Å2
3---2.02 Å2
Refinement stepCycle: 1 / Resolution: 1.34→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1246 0 26 236 1508
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0350.0191333
X-RAY DIFFRACTIONr_bond_other_d0.0020.021182
X-RAY DIFFRACTIONr_angle_refined_deg1.8031.9331769
X-RAY DIFFRACTIONr_angle_other_deg1.22932707
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3965158
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.04823.17563
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.28615191
X-RAY DIFFRACTIONr_dihedral_angle_4_deg8.52157
X-RAY DIFFRACTIONr_chiral_restr0.350.2181
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021506
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02336
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.7581.869647
X-RAY DIFFRACTIONr_mcbond_other1.7211.864642
X-RAY DIFFRACTIONr_mcangle_it2.0252.811792
X-RAY DIFFRACTIONr_mcangle_other2.0242.813793
X-RAY DIFFRACTIONr_scbond_it2.0212.137686
X-RAY DIFFRACTIONr_scbond_other2.022.137687
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.3033.126978
X-RAY DIFFRACTIONr_long_range_B_refined3.8518.2211715
X-RAY DIFFRACTIONr_long_range_B_other3.20716.8481569
X-RAY DIFFRACTIONr_rigid_bond_restr3.3132514
X-RAY DIFFRACTIONr_sphericity_free26.636549
X-RAY DIFFRACTIONr_sphericity_bonded8.86452641
LS refinement shellResolution: 1.344→1.379 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.305 188 -
Rwork0.289 2261 -
obs--91.28 %

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