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- PDB-1rm8: Crystal structure of the catalytic domain of MMP-16/MT3-MMP: Char... -

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Basic information

Entry
Database: PDB / ID: 1rm8
TitleCrystal structure of the catalytic domain of MMP-16/MT3-MMP: Characterization of MT-MMP specific features
ComponentsMatrix metalloproteinase-16
KeywordsHYDROLASE / MMP-16 / MT3-MMP / MT-MMP / Membrane Type - Matrix Metalloproteinase / Batimastat / Hydroxamate inhibitor / Protease
Function / homology
Function and homology information


craniofacial suture morphogenesis / chondrocyte proliferation / endochondral ossification / protein metabolic process / embryonic cranial skeleton morphogenesis / Hydrolases; Acting on peptide bonds (peptidases); Metalloendopeptidases / Activation of Matrix Metalloproteinases / metalloaminopeptidase activity / plasma membrane => GO:0005886 / enzyme activator activity ...craniofacial suture morphogenesis / chondrocyte proliferation / endochondral ossification / protein metabolic process / embryonic cranial skeleton morphogenesis / Hydrolases; Acting on peptide bonds (peptidases); Metalloendopeptidases / Activation of Matrix Metalloproteinases / metalloaminopeptidase activity / plasma membrane => GO:0005886 / enzyme activator activity / collagen catabolic process / extracellular matrix disassembly / extracellular matrix / extracellular matrix organization / skeletal system development / metalloendopeptidase activity / protein processing / Golgi lumen / cell surface / proteolysis / zinc ion binding / plasma membrane
Similarity search - Function
Matrix metalloproteinase-16 / Peptidase M10A, matrix metallopeptidase, C-terminal / Domain of unknown function (DUF3377) / 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 ...Matrix metalloproteinase-16 / Peptidase M10A, matrix metallopeptidase, C-terminal / Domain of unknown function (DUF3377) / 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 / Matrix metalloproteinase-16
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsLang, R. / Braun, M. / Sounni, N.E. / Noel, A. / Frankenne, F. / Foidart, J.-M. / Bode, W. / Maskos, K.
CitationJournal: J.Mol.Biol. / Year: 2004
Title: Crystal structure of the catalytic domain of MMP-16/MT3-MMP: characterization of MT-MMP specific features.
Authors: Lang, R. / Braun, M. / Sounni, N.E. / Noel, A. / Frankenne, F. / Foidart, J.M. / Bode, W. / Maskos, K.
History
DepositionNov 27, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 9, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 8, 2017Group: Structure summary
Revision 1.4Jul 28, 2021Group: Advisory / Derived calculations / Refinement description
Category: pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms ...pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues / refine / struct_conn / struct_site
Item: _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_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_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 / _refine.ls_percent_reflns_obs / _refine.pdbx_ls_cross_valid_method / _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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Aug 23, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Matrix metalloproteinase-16
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,5636
Polymers18,8751
Non-polymers6895
Water2,072115
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)51.210, 51.210, 149.368
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number95
Cell settingtetragonal
Space group name H-MP4322

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Components

#1: Protein Matrix metalloproteinase-16 / / E.C.3.4.24.- / MMP-16 / MT3-MMP / Membrane-type matrix metalloproteinase 3 / MT-MMP 3 / MTMMP3 / Membrane-type-3 ...MMP-16 / MT3-MMP / Membrane-type matrix metalloproteinase 3 / MT-MMP 3 / MTMMP3 / Membrane-type-3 matrix metalloproteinase / MT3MMP / MMP-X2


Mass: 18874.764 Da / Num. of mol.: 1 / Fragment: catalytic domain
Source method: isolated from a genetically manipulated source
Details: complexed with Batimastat (bb94) / Source: (gene. exp.) Homo sapiens (human) / Plasmid: pT7cdMP3 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21
References: UniProt: P51512, Hydrolases; Acting on peptide bonds (peptidases); Metalloendopeptidases
#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.: 2 / 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 / Batimastat


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


Mass: 18.015 Da / Num. of mol.: 115 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.59 Å3/Da / Density % sol: 52.55 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: Tris-HCl, Sodium/potassium tartrate, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal grow
*PLUS
Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
150 mMTris-HCl1droppH8.5
2100 mM1dropNaCl
35 mM1dropCaCl2
410 mg/mlcdMT3-MMP1drop
50.5 mg/mlbatimastat1drop
6100 mMTris-HCl1reservoirpH8.7
71.1 Msodium phosphate-tartrate1reservoir

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
12931
21001
Diffraction source
SourceSiteBeamlineTypeIDWavelength (Å)
ROTATING ANODERIGAKU RU30011.5418
SYNCHROTRONMPG/DESY, HAMBURG BW621.0503
Detector
TypeIDDetectorDateDetails
MARRESEARCH1IMAGE PLATEApr 7, 1999mirrors
MARRESEARCH2CCDSep 18, 1999
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.54181
21.05031
ReflectionResolution: 1.8→16.6 Å / Num. obs: 18455 / % possible obs: 96.7 % / Observed criterion σ(I): 2.2 / Biso Wilson estimate: 23.51 Å2 / Rsym value: 0.083 / Net I/σ(I): 5.5
Reflection shellResolution: 1.8→1.9 Å / Rmerge(I) obs: 0.327 / Mean I/σ(I) obs: 2.2 / Num. unique all: 1090 / Rsym value: 0.327 / % possible all: 91.1
Reflection
*PLUS
Lowest resolution: 16.6 Å / Num. measured all: 119029 / Rmerge(I) obs: 0.083
Reflection shell
*PLUS
Highest resolution: 1.8 Å / Lowest resolution: 1.9 Å / % possible obs: 91.1 %

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
REFMAC5refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Pdb code 1bqq

1bqq


Resolution: 1.8→16.6 Å / Isotropic thermal model: overall temperature factors / Cross valid method: FREE R-VALUE / σ(F): 1 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.23644 900 -Random
Rwork0.20768 ---
all0.20907 ---
obs0.20907 18455 96.7 %-
Displacement parametersBiso mean: 23.509 Å2
Baniso -1Baniso -2Baniso -3
1-0.07 Å20 Å20 Å2
2--0.07 Å20 Å2
3----0.15 Å2
Refinement stepCycle: LAST / Resolution: 1.8→16.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1338 0 36 115 1489
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_refined_d0.017
X-RAY DIFFRACTIONr_angle_refined_deg1.712
Software
*PLUS
Version: 5 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 16.6 Å / Num. reflection obs: 17555 / % reflection Rfree: 4.9 % / Rfactor Rfree: 0.236 / Rfactor Rwork: 0.208
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONbond_d0.014
X-RAY DIFFRACTIONangle_d
X-RAY DIFFRACTIONangle_deg1.712

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