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- PDB-5h0u: Crystal structure of the catalytic domain of membrane type 1 matr... -

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Basic information

Entry
Database: PDB / ID: 5h0u
TitleCrystal structure of the catalytic domain of membrane type 1 matrix metalloproteinase
Components
  • HIS-HIS-HIS-HIS-HIS-HIS
  • Matrix metalloproteinase-14
KeywordsHYDROLASE / catalytic domain membrane type 1 matrix metalloproteinase MT1-MMP
Function / homology
Function and homology information


membrane-type matrix metalloproteinase-1 / negative regulation of GDF15-GFRAL signaling pathway / craniofacial suture morphogenesis / positive regulation of macrophage migration / macropinosome / head development / chondrocyte proliferation / astrocyte cell migration / response to odorant / tissue remodeling ...membrane-type matrix metalloproteinase-1 / negative regulation of GDF15-GFRAL signaling pathway / craniofacial suture morphogenesis / positive regulation of macrophage migration / macropinosome / head development / chondrocyte proliferation / astrocyte cell migration / response to odorant / tissue remodeling / negative regulation of focal adhesion assembly / positive regulation of protein processing / endochondral ossification / embryonic cranial skeleton morphogenesis / zymogen activation / endothelial cell proliferation / intermediate filament cytoskeleton / positive regulation of B cell differentiation / branching morphogenesis of an epithelial tube / positive regulation of myotube differentiation / negative regulation of Notch signaling pathway / Activation of Matrix Metalloproteinases / endodermal cell differentiation / metalloaminopeptidase activity / Collagen degradation / collagen catabolic process / extracellular matrix disassembly / regulation of protein localization to plasma membrane / response to mechanical stimulus / ovarian follicle development / Degradation of the extracellular matrix / extracellular matrix organization / extracellular matrix / skeletal system development / cell motility / lung development / protein catabolic process / response to organic cyclic compound / protein processing / metalloendopeptidase activity / Golgi lumen / response to estrogen / male gonad development / melanosome / integrin binding / cytoplasmic vesicle / positive regulation of cell growth / angiogenesis / endopeptidase activity / response to oxidative stress / response to hypoxia / positive regulation of cell migration / serine-type endopeptidase activity / focal adhesion / proteolysis / extracellular space / zinc ion binding / nucleus / plasma membrane / cytosol
Similarity search - Function
Peptidase M10A, matrix metallopeptidase, C-terminal / Domain of unknown function (DUF3377) / PGBD superfamily / 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 ...Peptidase M10A, matrix metallopeptidase, C-terminal / Domain of unknown function (DUF3377) / PGBD superfamily / 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
Matrix metalloproteinase-14
Similarity search - Component
Biological speciesHomo sapiens (human)
unidentified (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.239 Å
AuthorsOgata, H. / Decaneto, E. / Lubitz, W.
CitationJournal: Phys Chem Chem Phys / Year: 2017
Title: Solvent water interactions within the active site of the membrane type I matrix metalloproteinase.
Authors: Decaneto, E. / Vasilevskaya, T. / Kutin, Y. / Ogata, H. / Grossman, M. / Sagi, I. / Havenith, M. / Lubitz, W. / Thiel, W. / Cox, N.
History
DepositionOct 7, 2016Deposition site: PDBJ / Processing site: PDBE
Revision 1.0Oct 4, 2017Provider: repository / Type: Initial release
Revision 1.1Oct 11, 2017Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed ..._citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Nov 29, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Jan 10, 2024Group: 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
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_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Matrix metalloproteinase-14
B: HIS-HIS-HIS-HIS-HIS-HIS
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,43716
Polymers20,1852
Non-polymers1,25114
Water1,22568
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3330 Å2
ΔGint-85 kcal/mol
Surface area9000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.995, 62.995, 122.620
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

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Protein / Protein/peptide , 2 types, 2 molecules AB

#1: Protein Matrix metalloproteinase-14 / MMP-14 / MMP-X1 / Membrane-type matrix metalloproteinase 1 / MTMMP1 / Membrane-type-1 matrix ...MMP-14 / MMP-X1 / Membrane-type matrix metalloproteinase 1 / MTMMP1 / Membrane-type-1 matrix metalloproteinase / MT1MMP


Mass: 19338.320 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MMP14 / Production host: Escherichia coli (E. coli)
References: UniProt: P50281, membrane-type matrix metalloproteinase-1
#2: Protein/peptide HIS-HIS-HIS-HIS-HIS-HIS


Mass: 846.896 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: His-tag / Source: (gene. exp.) unidentified (others) / Production host: Escherichia coli (E. coli)

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Non-polymers , 5 types, 82 molecules

#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn
#5: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C8H18N2O4S / Comment: pH buffer*YM
#6: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C3H8O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 68 / 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: 3.04 Å3/Da / Density % sol: 59.49 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / Details: Ammonium nitrate, PEG3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.91841 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Aug 2, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91841 Å / Relative weight: 1
ReflectionResolution: 2.239→44.544 Å / Num. obs: 12491 / % possible obs: 99.8 % / Redundancy: 7.9 % / Rmerge(I) obs: 0.105 / Net I/σ(I): 16.8
Reflection shellResolution: 2.239→2.37 Å / Rmerge(I) obs: 0.998 / Mean I/σ(I) obs: 2.3 / % possible all: 99.3

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Processing

Software
NameVersionClassification
PHENIX(1.10_2140: ???)refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1BQQ

1bqq


Resolution: 2.239→44.544 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 26.11
RfactorNum. reflection% reflection
Rfree0.2538 625 5 %
Rwork0.1953 --
obs0.1982 12491 99.78 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.239→44.544 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1431 0 68 68 1567
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071537
X-RAY DIFFRACTIONf_angle_d1.0082074
X-RAY DIFFRACTIONf_dihedral_angle_d17.136861
X-RAY DIFFRACTIONf_chiral_restr0.054194
X-RAY DIFFRACTIONf_plane_restr0.006271
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2389-2.46420.34481520.25442879X-RAY DIFFRACTION100
2.4642-2.82080.29561530.23142909X-RAY DIFFRACTION100
2.8208-3.55360.2451550.20222958X-RAY DIFFRACTION100
3.5536-44.5530.22971650.17083120X-RAY DIFFRACTION100

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