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- PDB-1cxv: STRUCTURE OF RECOMBINANT MOUSE COLLAGENASE-3 (MMP-13) -

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Basic information

Entry
Database: PDB / ID: 1cxv
TitleSTRUCTURE OF RECOMBINANT MOUSE COLLAGENASE-3 (MMP-13)
ComponentsPROTEIN (COLLAGENASE-3)
KeywordsHYDROLASE / METALLOPROTEASE / GLYCOPROTEIN / COLLAGEN DEGRADATION
Function / homology
Function and homology information


positive regulation of pancreatic trypsinogen secretion / Activation of Matrix Metalloproteinases / Collagen degradation / Assembly of collagen fibrils and other multimeric structures / protein metabolic process => GO:0019538 / growth plate cartilage development / Degradation of the extracellular matrix / endochondral ossification / intercellular canaliculus / Hydrolases; Acting on peptide bonds (peptidases); Metalloendopeptidases ...positive regulation of pancreatic trypsinogen secretion / Activation of Matrix Metalloproteinases / Collagen degradation / Assembly of collagen fibrils and other multimeric structures / protein metabolic process => GO:0019538 / growth plate cartilage development / Degradation of the extracellular matrix / endochondral ossification / intercellular canaliculus / Hydrolases; Acting on peptide bonds (peptidases); Metalloendopeptidases / bone morphogenesis / cartilage development / low-density lipoprotein particle receptor binding / peptide catabolic process / bone mineralization / fibronectin binding / collagen catabolic process / extracellular matrix disassembly / collagen binding / extracellular matrix organization / extracellular matrix / response to hormone / metalloendopeptidase activity / calcium-dependent protein binding / heart development / peptidase activity / endopeptidase activity / lysosome / calcium ion binding / Golgi apparatus / proteolysis / extracellular space / zinc ion binding / extracellular region
Similarity search - Function
Collagenase 3 / 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 ...Collagenase 3 / 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
Chem-CBP / Collagenase 3
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / Resolution: 2 Å
AuthorsBotos, I. / Meyer, E. / Swanson, S.M. / Lemaitre, V. / Eeckhout, Y. / Meyer, E.F.
Citation
Journal: J.Mol.Biol. / Year: 1999
Title: Structure of recombinant mouse collagenase-3 (MMP-13).
Authors: Botos, I. / Meyer, E. / Swanson, S.M. / Lemaitre, V. / Eeckhout, Y. / Meyer, E.F.
#1: Journal: Nat.Struct.Biol. / Year: 1999
Title: Crystal Structures of Mmp-1 and-13 Reveal the Structural Basis for Selectivity of Collagenase Inhibitors
Authors: Lovejoy, B. / Welch, A.R. / Carr, S. / Luong, C. / Broka, C. / Hendriks, T. / Campbell, J.A. / Walker, K.A.M. / Martin, R. / Van, W.H. / Browner, M.F.
#2: Journal: Biochem.Biophys.Res.Commun. / Year: 1997
Title: The Recombinant Catalytic Domain of Mouse Collagenase-3 Depolymerizes Type I Collagen by Cleaving its Aminotelopeptides
Authors: Lemaitre, V. / Jungbluth, A. / Eeckhout, Y.
History
DepositionAug 30, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 30, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 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_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.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.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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PROTEIN (COLLAGENASE-3)
B: PROTEIN (COLLAGENASE-3)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,31512
Polymers37,0412
Non-polymers1,27410
Water5,783321
1
A: PROTEIN (COLLAGENASE-3)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,1576
Polymers18,5211
Non-polymers6375
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: PROTEIN (COLLAGENASE-3)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,1576
Polymers18,5211
Non-polymers6375
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)56.360, 48.460, 74.940
Angle α, β, γ (deg.)90.00, 108.15, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein PROTEIN (COLLAGENASE-3) / MATRIX METALLOPROTEINASE / MMP-13


Mass: 18520.551 Da / Num. of mol.: 2 / Fragment: CATALYTIC DOMAIN / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)
References: UniProt: P33435, Hydrolases; Acting on peptide bonds (peptidases); Metalloendopeptidases
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-CBP / 2-{4-[4-(4-CHLORO-PHENOXY)-BENZENESULFONYL]-TETRAHYDRO-PYRAN-4-YL}-N-HYDROXY-ACETAMIDE


Mass: 425.883 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C19H20ClNO6S
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 321 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.62 Å3/Da / Density % sol: 53.12 %
Crystal grow
*PLUS
Temperature: 18 ℃ / pH: 7.5 / Method: batch method
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
117 mg/mlprotein11
210 mMHEPES11
3ammonium sulfate11saturated

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Data collection

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionBiso Wilson estimate: 14.8 Å2
Reflection
*PLUS
Highest resolution: 2 Å / Lowest resolution: 30 Å / Num. obs: 25433 / % possible obs: 96.8 % / Num. measured all: 165387 / Rmerge(I) obs: 0.075
Reflection shell
*PLUS
Highest resolution: 2 Å / Lowest resolution: 2.07 Å / % possible obs: 94.3 % / Rmerge(I) obs: 0.286 / Mean I/σ(I) obs: 2.8

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Processing

SoftwareName: CNS / Version: 0.5 / Classification: refinement
RefinementResolution: 2→30 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 490456.23 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.234 2233 9.9 %RANDOM
Rwork0.196 ---
obs0.196 22560 85.9 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 35.88 Å2 / ksol: 0.327 e/Å3
Displacement parametersBiso mean: 28.8 Å2
Baniso -1Baniso -2Baniso -3
1-2.37 Å20 Å24.51 Å2
2---0.23 Å20 Å2
3----2.14 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.28 Å0.23 Å
Luzzati d res low-5 Å
Luzzati sigma a0.17 Å0.16 Å
Refinement stepCycle: LAST / Resolution: 2→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2568 0 64 321 2953
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg2.1
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d23.6
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.76
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it0.671.5
X-RAY DIFFRACTIONc_mcangle_it1.212
X-RAY DIFFRACTIONc_scbond_it0.772
X-RAY DIFFRACTIONc_scangle_it1.272.5
Refine LS restraints NCSNCS model details: CONSTR
LS refinement shellResolution: 2→2.13 Å / Rfactor Rfree error: 0.014 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.257 333 10.7 %
Rwork0.229 2779 -
obs--71.7 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PAPROTEIN.TOP
X-RAY DIFFRACTION2RS.PARAMRS.TOP
X-RAY DIFFRACTION3WATER_REP.PARAWATER.TOP
X-RAY DIFFRACTION4ZN.PARAMZN.TOP
Software
*PLUS
Version: 0.5 / Classification: refinement
Refinement
*PLUS
σ(F): 2 / % reflection Rfree: 9.9 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 28.8 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_angle_deg2.1
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg23.6
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.76
X-RAY DIFFRACTIONc_mcbond_it1.5
X-RAY DIFFRACTIONc_scbond_it2
X-RAY DIFFRACTIONc_mcangle_it2
X-RAY DIFFRACTIONc_scangle_it2.5
LS refinement shell
*PLUS
Rfactor Rfree: 0.257 / % reflection Rfree: 10.7 % / Rfactor Rwork: 0.229

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