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- PDB-1rmz: Crystal structure of the catalytic domain of human MMP12 complexe... -

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Basic information

Entry
Database: PDB / ID: 1rmz
TitleCrystal structure of the catalytic domain of human MMP12 complexed with the inhibitor NNGH at 1.3 A resolution
ComponentsMacrophage metalloelastase
KeywordsHYDROLASE / MATRIX METALLOPROTEINASE / MMP12 / ELASTASE / COMPLEX (ELASTASE-INHIBITOR) / METALLO ELASTASE / NNGH
Function / homology
Function and homology information


macrophage elastase / negative regulation of endothelial cell-matrix adhesion / 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 / 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 / Collagen degradation / collagen catabolic process / positive regulation of interferon-alpha production / 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 / extracellular region / zinc ion binding / 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
AuthorsBertini, I. / Calderone, V. / Fragai, M. / Luchinat, C. / Mangani, S. / Terni, B.
Citation
Journal: Proc.Natl.Acad.Sci.Usa / 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.
#1: Journal: ANGEW.CHEM.INT.ED.ENGL. / Year: 2003
Title: X-ray Structures of Binary and Ternary Enzyme-Product-Inhibitor Complexes of Matrix Metalloproteinases
Authors: Bertini, I. / Calderone, V. / Fragai, M. / Luchinat, C. / Mangani, S. / Terni, B.
#2: Journal: J.Mol.Biol. / Year: 2001
Title: Substrate specificity determinants of human macrophage elastase (MMP-12) based on the 1.1 A crystal structure
Authors: Lang, R. / Kocourek, A. / Braun, M. / Tschesche, H. / Huber, R. / Bode, W. / Maskos, K.
History
DepositionNov 28, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 14, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 27, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / 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_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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Aug 23, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)69.194, 62.564, 37.262
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-353-

HOH

DetailsThe protein is monomeric in vivo and there is one molecule in the asymmetric unit.

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Components

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


Mass: 17615.670 Da / Num. of mol.: 1 / Mutation: F171D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MMP12, HME / Plasmid: pET21 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / 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

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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 / Details: double-crystal monochromator Si(111) and Si(220)
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. all: 36295 / Num. obs: 36295 / % possible obs: 98.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.2 % / Biso Wilson estimate: 16.389 Å2 / Rmerge(I) obs: 0.057 / Rsym value: 0.057 / 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 / Num. unique all: 4889 / Rsym value: 0.308 / % possible all: 92.6

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 1OS9

1os9


Resolution: 1.34→20 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.954 / SU B: 1.097 / SU ML: 0.045 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.067 / ESU R Free: 0.063 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2149 2578 7.1 %RANDOM
Rwork0.17857 ---
all0.18111 33678 --
obs0.18111 33678 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 18.214 Å2
Baniso -1Baniso -2Baniso -3
1--1.38 Å20 Å20 Å2
2---0.72 Å20 Å2
3---2.1 Å2
Refine analyzeLuzzati coordinate error obs: 0.045 Å
Refinement stepCycle: LAST / 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_d0.0140.0211301
X-RAY DIFFRACTIONr_bond_other_d0.0020.021128
X-RAY DIFFRACTIONr_angle_refined_deg1.6681.9291762
X-RAY DIFFRACTIONr_angle_other_deg1.00632616
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4165158
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1970.2184
X-RAY DIFFRACTIONr_gen_planes_refined0.010.021470
X-RAY DIFFRACTIONr_gen_planes_other0.0090.02292
X-RAY DIFFRACTIONr_nbd_refined0.2170.2317
X-RAY DIFFRACTIONr_nbd_other0.2460.21388
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.0870.2739
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1810.2139
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.1070.221
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2210.215
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2840.250
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2170.222
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_mcbond_it1.3731.5782
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.06721248
X-RAY DIFFRACTIONr_scbond_it2.4613519
X-RAY DIFFRACTIONr_scangle_it3.534.5514
X-RAY DIFFRACTIONr_rigid_bond_restr1.35221301
X-RAY DIFFRACTIONr_sphericity_free3.8992247
X-RAY DIFFRACTIONr_sphericity_bonded3.01221264
LS refinement shellResolution: 1.34→1.379 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.263 186
Rwork0.248 2251

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