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- PDB-3uvc: MMP12 in a complex with the dimeric adduct: 5-(5-phenylhydantoin)... -

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Basic information

Entry
Database: PDB / ID: 3uvc
TitleMMP12 in a complex with the dimeric adduct: 5-(5-phenylhydantoin)-5-phenylhydantoin
ComponentsMacrophage metalloelastase
KeywordsHYDROLASE / metalloprotease
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 / Collagen degradation / collagen catabolic process / extracellular matrix disassembly / positive regulation of interferon-alpha production / 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-0D2 / IMIDAZOLE / Macrophage metalloelastase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.3 Å
AuthorsDerbyshire, D.J. / Danielson, H. / Nystrum, S.
CitationJournal: To be Published
Title: Characterization of fragments interacting with MMP-12
Authors: Nordstrom, H. / Gossas, T. / Derbyshire, D.J. / Danielson, H.
History
DepositionNov 29, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 2, 2013Provider: repository / Type: Initial release
Revision 1.1Feb 28, 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_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_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 1.2Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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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)38,26729
Polymers36,5612
Non-polymers1,70627
Water8,827490
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A: Macrophage metalloelastase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,36316
Polymers18,2801
Non-polymers1,08315
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Macrophage metalloelastase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,90413
Polymers18,2801
Non-polymers62312
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)39.746, 60.625, 58.403
Angle α, β, γ (deg.)90.00, 103.10, 90.00
Int Tables number4
Space group name H-MP1211

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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: 18280.455 Da / Num. of mol.: 2 / Fragment: CATALYTIC DOMAIN, RESIDUES 106-263 / Mutation: E216A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: 4321, HME, MMP12 / Plasmid: Pet11a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P39900, macrophage elastase

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Non-polymers , 7 types, 517 molecules

#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Ca
#4: Chemical
ChemComp-IMD / IMIDAZOLE


Mass: 69.085 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H5N2
#5: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Cl
#6: Chemical ChemComp-0D2 / (4R,4'S)-4,4'-diphenyl-4,4'-biimidazolidine-2,2',5,5'-tetrone


Mass: 350.328 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H14N4O4
#7: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 490 / 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: 1.87 Å3/Da / Density % sol: 34.38 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 50mM imidazole pH 7.5, 200-400mM CaCl, 20% PEG 1k, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 1.07225 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 25, 2008
RadiationMonochromator: Silicon (1 1 1) channel-cut, silicon toroidal mirror coated with Rhodium
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.07225 Å / Relative weight: 1
ReflectionResolution: 1.3→41.487 Å / Num. all: 65111 / Num. obs: 65111 / % possible obs: 98.2 % / Redundancy: 2.8 % / Rmerge(I) obs: 0.08 / Rsym value: 0.08 / Net I/σ(I): 6.9
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.3-1.372.10.6351.21793385790.63589.1
1.37-1.452.90.4671.62626991250.46799.8
1.45-1.552.90.2922.52518785540.29299.9
1.55-1.6830.1863.92370180240.186100
1.68-1.8430.13552172773360.13599.9
1.84-2.0630.097.21974566780.0999.9
2.06-2.372.90.0689.11729058750.06899.8
2.37-2.912.90.0728.21427149940.07299.5
2.91-4.112.80.05211.51089638590.05299.8
4.11-41.48730.04214.9632620870.04296.3

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 44.38 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å41.48 Å
Translation2.5 Å41.48 Å

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALA3.2.25data scaling
PHASER2.1.4phasing
REFMACrefinement
PDB_EXTRACT3.1data extraction
ADSCQuantumdata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: internal model: V108-L261 no metal ions.

Resolution: 1.3→41.487 Å / Cor.coef. Fo:Fc: 0.981 / Cor.coef. Fo:Fc free: 0.962 / WRfactor Rfree: 0.1836 / WRfactor Rwork: 0.1327 / Occupancy max: 1 / Occupancy min: 0 / FOM work R set: 0.889 / SU B: 1.931 / SU ML: 0.036 / SU R Cruickshank DPI: 0.0537 / SU Rfree: 0.0522 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.054 / ESU R Free: 0.052 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1736 3294 5.1 %RANDOM
Rwork0.1302 ---
obs0.1324 64982 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 max: 94.86 Å2 / Biso mean: 19.7329 Å2 / Biso min: 8.93 Å2
Baniso -1Baniso -2Baniso -3
1--0.93 Å20 Å2-0.22 Å2
2--0.93 Å20 Å2
3----0.1 Å2
Refinement stepCycle: LAST / Resolution: 1.3→41.487 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2451 0 78 490 3019
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0212776
X-RAY DIFFRACTIONr_angle_refined_deg1.4651.9343793
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5675368
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.98122.538130
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.43815411
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.4191517
X-RAY DIFFRACTIONr_chiral_restr0.0910.2391
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0212218
X-RAY DIFFRACTIONr_mcbond_it1.2991.51642
X-RAY DIFFRACTIONr_mcangle_it2.05522653
X-RAY DIFFRACTIONr_scbond_it2.69531134
X-RAY DIFFRACTIONr_scangle_it3.7244.51114
X-RAY DIFFRACTIONr_rigid_bond_restr1.30132776
LS refinement shellResolution: 1.3→1.334 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.269 217 -
Rwork0.273 3826 -
all-4043 -
obs--100 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.0027-0.0007-0.00030.0008-0.00030.0108-0.0002-0.00040-0.000200-0.0006-0.00020.00020.0118-0.0002-0.00170.00110.00030.01189.0607-12.495119.2886
20.06360.01010.00830.00130.00420.0225-0.00080.00240.0024-0.00030.00050-0.00210.00090.00030.01180.0005-0.00160-0.00050.011612.3424-12.2679-9.688
31.24730.0217-0.3302-0.1659-0.0913-0.1582-0.00520.0008-0.019-0.00760.0126-0.0075-0.00650.0145-0.00740.0126-0.0007-0.00210.0056-0.00010.011413.5919-6.465611.5403
40.00140.0001-0.00090.00120.00160.0048-0.00020.00010.00030.00040-0.0003-0.00030.00010.00010.01170.0001-0.00180.004500.011710.5065-13.05386.6874
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A106 - 263
2X-RAY DIFFRACTION1A301 - 313
3X-RAY DIFFRACTION2B105 - 263
4X-RAY DIFFRACTION2B301 - 312
5X-RAY DIFFRACTION3A314
6X-RAY DIFFRACTION4A401 - 673
7X-RAY DIFFRACTION4B401 - 617

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