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- PDB-1jk3: Crystal structure of human MMP-12 (Macrophage Elastase) at true a... -

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Basic information

Entry
Database: PDB / ID: 1jk3
TitleCrystal structure of human MMP-12 (Macrophage Elastase) at true atomic resolution
ComponentsMACROPHAGE METALLOELASTASE
KeywordsHYDROLASE / Matrix metalloproteinase / batimastat / bb94 / hydroxamic acid / MMP12 / elastase / complex (elastase-inhibitor) / metallo elastase
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 / extracellular matrix organization / 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-BAT / Macrophage metalloelastase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.09 Å
AuthorsLang, R. / Kocourek, A. / Braun, M. / Tschesche, H. / Huber, R. / Bode, W. / Maskos, K.
CitationJournal: 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
DepositionJul 11, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 28, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / 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_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_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_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.pdbx_ptnr2_label_alt_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_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 16, 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)18,1877
Polymers17,4591
Non-polymers7296
Water3,765209
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: MACROPHAGE METALLOELASTASE
hetero molecules

A: MACROPHAGE METALLOELASTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,37414
Polymers34,9172
Non-polymers1,45712
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Buried area3830 Å2
ΔGint-135 kcal/mol
Surface area14440 Å2
MethodPISA
3
A: MACROPHAGE METALLOELASTASE
hetero molecules

A: MACROPHAGE METALLOELASTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,37414
Polymers34,9172
Non-polymers1,45712
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
MethodPQS
Unit cell
Length a, b, c (Å)51.905, 60.263, 54.612
Angle α, β, γ (deg.)90.00, 114.65, 90.00
Int Tables number5
Cell settingmonoclinic
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-900-

BAT

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Components

#1: Protein MACROPHAGE METALLOELASTASE / E.C.3.4.24.65 / MMP-12 / HME / MATRIX METALLOPROTEINASE-12 / MMP-12 / metalloelastase HME


Mass: 17458.525 Da / Num. of mol.: 1 / Fragment: catalytic domain / Mutation: E219A
Source method: isolated from a genetically manipulated source
Details: complexed with Batimastat (BB94), residue BAT / Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / 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-BAT / 4-(N-HYDROXYAMINO)-2R-ISOBUTYL-2S-(2-THIENYLTHIOMETHYL)SUCCINYL-L-PHENYLALANINE-N-METHYLAMIDE / BATIMASTAT / BB94


Mass: 477.640 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C23H31N3O4S2 / Comment: inhibitor*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 209 / 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: 2.22 Å3/Da / Density % sol: 44.66 %
Crystal growTemperature: 273 K / Method: vapor diffusion, sitting drop / pH: 6.4
Details: LiCl, MES, pH 6.4, VAPOR DIFFUSION, SITTING DROP at 273K
Crystal grow
*PLUS
pH: 8.5
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
14 mg/mlcdMMP-121drop
21 mg/mlbatimastat1drop
31*10-6 mMinhibitor1drop
45 mMTris1drop
550 mM1dropNaCl
65 mM1dropCaCl2
7100 mMMES1reservoir
8100 mM1reservoirLiCl

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MPG/DESY, HAMBURG / Beamline: BW6 / Wavelength: 1.0503 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Apr 10, 2000
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0503 Å / Relative weight: 1
ReflectionResolution: 1.09→22.36 Å / Num. obs: 60360 / % possible obs: 95 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rsym value: 0.063 / Net I/σ(I): 12.68
Reflection shellResolution: 1.09→1.13 Å / Mean I/σ(I) obs: 3.2 / Rsym value: 0.256 / % possible all: 91.9
Reflection
*PLUS
Num. measured all: 359642 / Rmerge(I) obs: 0.063
Reflection shell
*PLUS
% possible obs: 91.9 % / Rmerge(I) obs: 0.256

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Processing

Software
NameClassification
AMoREphasing
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1UEA

1uea


Resolution: 1.09→22.36 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.962 / SU B: 1.1 / SU ML: 0.029 / SU Rfree: 0.036 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.035 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.19572 3044 5 %RANDOM
Rwork0.16742 ---
all0.16881 60360 --
obs0.16881 57313 100 %-
Displacement parametersBiso mean: 11.976 Å2
Baniso -1Baniso -2Baniso -3
1--0.11 Å20 Å2-0.21 Å2
2---0.08 Å20 Å2
3---0.02 Å2
Refinement stepCycle: LAST / Resolution: 1.09→22.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1237 0 37 209 1483
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONp_bond_d0.0130.0211378
X-RAY DIFFRACTIONp_angle_d1.8751.9451871
X-RAY DIFFRACTIONp_mcbond_it1.3841.5790
X-RAY DIFFRACTIONp_mcangle_it2.0921285
X-RAY DIFFRACTIONp_scbond_it2.4893588
X-RAY DIFFRACTIONp_scangle_it3.5344.5585
LS refinement shellResolution: 1.091→1.12 Å / Total num. of bins used: 20
RfactorNum. reflection
Rfree0.255 224
Rwork0.245 4183
all-4407
Software
*PLUS
Name: REFMAC / Classification: refinement
Refinement
*PLUS
σ(F): 0 / % reflection Rfree: 5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS

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