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- PDB-4h30: Crystal structure of the catalytic domain of MMP-12 in complex wi... -

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Basic information

Entry
Database: PDB / ID: 4h30
TitleCrystal structure of the catalytic domain of MMP-12 in complex with a twin inhibitor.
ComponentsMacrophage metalloelastase
Keywordshydrolase/hydrolase inhibitor / divalent inhibitor / carboxylic twin inhibitor / Dimerisation / METZINCIN / Zinc protease / hydrolase-hydrolase inhibtior complex / hydrolase-hydrolase inhibitor complex
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 / positive regulation of interferon-alpha production / response to amyloid-beta / 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 / cellular response to virus / metalloendopeptidase activity / 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
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-0ZD / DI(HYDROXYETHYL)ETHER / Macrophage metalloelastase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.43 Å
AuthorsAntoni, C. / Stura, E.A. / Vera, L. / Nuti, E. / Carafa, L. / Cassar-Lajeunesse, E. / Dive, V. / Rossello, A.
CitationJournal: J.Struct.Biol. / Year: 2013
Title: Crystallization of bi-functional ligand protein complexes.
Authors: Antoni, C. / Vera, L. / Devel, L. / Catalani, M.P. / Czarny, B. / Cassar-Lajeunesse, E. / Nuti, E. / Rossello, A. / Dive, V. / Stura, E.A.
History
DepositionSep 13, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 24, 2013Provider: repository / Type: Initial release
Revision 1.1May 1, 2013Group: Database references
Revision 1.2Oct 8, 2014Group: Database references
Revision 1.3Aug 12, 2015Group: Database references
Revision 1.4Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / 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_alt_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_asym_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_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_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.pdbx_ptnr1_label_alt_id / _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_asym_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_ref_seq_dif.details / _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: Macrophage metalloelastase
B: Macrophage metalloelastase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,45922
Polymers35,2312
Non-polymers2,22820
Water8,233457
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4250 Å2
ΔGint-97 kcal/mol
Surface area15200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.910, 61.750, 112.560
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 2 molecules AB

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


Mass: 17615.670 Da / Num. of mol.: 2
Fragment: Human MMP12 catalytic domain (unp residues 106-263)
Mutation: F171D
Source method: isolated from a genetically manipulated source
Details: catalytic domain active / Source: (gene. exp.) Homo sapiens (human) / Gene: HME, MMP12 / Plasmid: PET24A / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P39900, macrophage elastase

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Non-polymers , 6 types, 477 molecules

#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: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-0ZD / N,N'-bis(2-[(biphenyl-4ylsulfonyl)[(2R)-1-hydroxy-3-methyl-1-oxobutan-2-yl]-amino]ethyl)benzene-1,3-dicarboxamide


Mass: 883.040 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C46H50N4O10S2
#6: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 457 / 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: 2.31 Å3/Da / Density % sol: 46.84 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: Protein: hMMP12 F171D at 0.36 milli-M + 0.001 M AHA. Reservoir: 13% PEG 20,000 0.2 M imidazole malate 0.05 M NaCl Cryoprotectant: 27% PEG 8,000 15% MPEG 550, 10% glycerol, 0.09 M Tris-HCl , ...Details: Protein: hMMP12 F171D at 0.36 milli-M + 0.001 M AHA. Reservoir: 13% PEG 20,000 0.2 M imidazole malate 0.05 M NaCl Cryoprotectant: 27% PEG 8,000 15% MPEG 550, 10% glycerol, 0.09 M Tris-HCl , pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.8856 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 1, 2012 / Details: mirrors
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8856 Å / Relative weight: 1
ReflectionResolution: 1.43→50 Å / Num. all: 61962 / Num. obs: 61752 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 5.82 % / Biso Wilson estimate: 21.616 Å2 / Rmerge(I) obs: 0.059 / Rsym value: 0.053 / Net I/σ(I): 19.29
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allRsym value% possible all
1.42-1.515.80.6262.7798800.5798.4
1.51-1.615.830.3824.692910.348100
1.61-1.745.840.2377.3786870.216100
1.74-1.916.010.13512.8179990.123100
1.91-2.145.940.07821.8873010.071100
2.14-2.465.890.05630.764430.051100
2.46-3.025.480.04240.0954870.03899.9
3.02-4.255.550.02953.7643500.02699.6
4.25-505.190.02757.7725240.02599.5

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Processing

Software
NameVersionClassification
DNAdata collection
MOLREPphasing
PHENIX(phenix.refine: 1.8_1069)refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4EFS

4efs


Resolution: 1.43→43.31 Å / SU ML: 0.1 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 1.99 / σ(I): -3 / Phase error: 15.92 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1767 3087 5 %RANDOM
Rwork0.1567 ---
obs0.1577 61749 99.66 %-
all-61752 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.43→43.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2492 0 127 457 3076
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062857
X-RAY DIFFRACTIONf_angle_d1.1183876
X-RAY DIFFRACTIONf_dihedral_angle_d16.2721012
X-RAY DIFFRACTIONf_chiral_restr0.078382
X-RAY DIFFRACTIONf_plane_restr0.006509
LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs% reflection obs (%)
1.4244-1.44670.2231290.2272460246094
1.4467-1.47040.25651410.206226752675100
1.4704-1.49580.20571390.196826282628100
1.4958-1.5230.21591390.185726422642100
1.523-1.55230.20211380.179926392639100
1.5523-1.5840.20231410.170226652665100
1.584-1.61840.2121390.166726362636100
1.6184-1.65610.17441380.164226302630100
1.6561-1.69750.21381380.1626152615100
1.6975-1.74340.1891400.157126732673100
1.7434-1.79470.18491400.155526632663100
1.7947-1.85260.18961400.155126522652100
1.8526-1.91880.17571400.146326622662100
1.9188-1.99560.16321410.148726782678100
1.9956-2.08650.18461400.141126502650100
2.0865-2.19650.17091400.144126732673100
2.1965-2.33410.17641420.152326922692100
2.3341-2.51430.18121410.156626792679100
2.5143-2.76720.15791430.156827192719100
2.7672-3.16760.18071420.158826982698100
3.1676-3.99040.16291450.140527602760100
3.9904-43.32020.15851510.16132873287399

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