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- PDB-1fbl: STRUCTURE OF FULL-LENGTH PORCINE SYNOVIAL COLLAGENASE (MMP1) REVE... -

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Basic information

Entry
Database: PDB / ID: 1fbl
TitleSTRUCTURE OF FULL-LENGTH PORCINE SYNOVIAL COLLAGENASE (MMP1) REVEALS A C-TERMINAL DOMAIN CONTAINING A CALCIUM-LINKED, FOUR-BLADED BETA-PROPELLER
ComponentsFIBROBLAST (INTERSTITIAL) COLLAGENASE (MMP-1)
KeywordsMETALLOPROTEASE
Function / homology
Function and homology information


Collagen degradation / Activation of Matrix Metalloproteinases / Degradation of the extracellular matrix / interstitial collagenase / Basigin interactions / cellular response to UV-A / collagen catabolic process / extracellular matrix organization / extracellular matrix / positive regulation of protein-containing complex assembly ...Collagen degradation / Activation of Matrix Metalloproteinases / Degradation of the extracellular matrix / interstitial collagenase / Basigin interactions / cellular response to UV-A / collagen catabolic process / extracellular matrix organization / extracellular matrix / positive regulation of protein-containing complex assembly / metalloendopeptidase activity / peptidase activity / proteolysis / extracellular region / zinc ion binding
Similarity search - Function
4 Propeller / Hemopexin / Hemopexin-like domain / Hemopexin, conserved site / Hemopexin domain signature. / Hemopexin-like domain / Peptidoglycan binding-like / Peptidase M10A, cysteine switch, zinc binding site / Matrixins cysteine switch. / Hemopexin-like repeats ...4 Propeller / Hemopexin / Hemopexin-like domain / Hemopexin, conserved site / Hemopexin domain signature. / Hemopexin-like domain / Peptidoglycan binding-like / Peptidase M10A, cysteine switch, zinc binding site / Matrixins cysteine switch. / Hemopexin-like repeats / Hemopexin-like domain superfamily / Hemopexin / Putative peptidoglycan binding domain / 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 / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Chem-HTA / Interstitial collagenase
Similarity search - Component
Biological speciesSus scrofa (pig)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.5 Å
AuthorsLi, J. / Brick, P. / Blow, D.M.
Citation
Journal: Structure / Year: 1995
Title: Structure of full-length porcine synovial collagenase reveals a C-terminal domain containing a calcium-linked, four-bladed beta-propeller.
Authors: Li, J. / Brick, P. / O'Hare, M.C. / Skarzynski, T. / Lloyd, L.F. / Curry, V.A. / Clark, I.M. / Bigg, H.F. / Hazleman, B.L. / Cawston, T.E. / Blow, D.M.
#1: Journal: J.Mol.Biol. / Year: 1989
Title: Crystallization and Preliminary X-Ray Analysis of Porcine Synovial Collagenase
Authors: Lloyd, L.F. / Skarzynski, T. / Wonacott, A.J. / Cawston, T.E. / Clark, I.M. / Mannix, C.J. / Harper, G.P.
History
DepositionApr 24, 1995Processing site: BNL
Revision 1.0Jan 29, 1996Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 22, 2012Group: Database references
Revision 1.4Nov 13, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / 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_entry_details.has_protein_modification / _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.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_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.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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: FIBROBLAST (INTERSTITIAL) COLLAGENASE (MMP-1)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,3598
Polymers42,6881
Non-polymers6717
Water5,314295
1
A: FIBROBLAST (INTERSTITIAL) COLLAGENASE (MMP-1)
hetero molecules

A: FIBROBLAST (INTERSTITIAL) COLLAGENASE (MMP-1)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,71816
Polymers85,3772
Non-polymers1,34114
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_665-x+1,-y+1,z1
Unit cell
Length a, b, c (Å)161.140, 161.140, 52.220
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number80
Space group name H-MI41

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Components

#1: Protein FIBROBLAST (INTERSTITIAL) COLLAGENASE (MMP-1)


Mass: 42688.355 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sus scrofa (pig) / Production host: Escherichia coli (E. coli) / References: UniProt: P21692, interstitial collagenase
#2: Chemical
ChemComp-CA / CALCIUM ION


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


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-HTA / N-[3-(N'-HYDROXYCARBOXAMIDO)-2-(2-METHYLPROPYL)-PROPANOYL]-O-TYROSINE-N-METHYLAMIDE


Mass: 379.451 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H29N3O5
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 295 / Source method: isolated from a natural source / Formula: H2O
Compound detailsTHE ENZYME CONSISTS OF AN N-TERMINAL CATALYTIC DOMAIN JOINED BY A LINKING PEPTIDE TO A C-TERMINAL ...THE ENZYME CONSISTS OF AN N-TERMINAL CATALYTIC DOMAIN JOINED BY A LINKING PEPTIDE TO A C-TERMINAL DOMAIN. THE MODEL FOR THE N-TERMINAL DOMAIN (RESIDUES 100 - 260) INCLUDES TWO ZINC IONS AND 3 CALCIUM IONS. ZINC 998 IS AT THE ACTIVE SITE AND COORDINATES HIS 218, HIS 222, AND HIS 228. ZINC 997 APPEARS TO HAVE A STRUCTURAL ROLE AND COORDINATES HIS 168, HIS 183, AND HIS 196. THE THREE CALCIUM IONS IN THE CATALYTIC DOMAIN ARE NUMBERED 993, 995, AND 996. THE LINKING PEPTIDE CONSISTS OF RESIDUE 261 - 277. THE C-TERMINAL HAEMOPEXIN LIKE DOMAIN CONSISTS OF RESIDUES 278 - 470 AND CONTAINS ONE ZINC ION LABELED AS 994.
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.97 Å3/Da / Density % sol: 69.01 %
Crystal
*PLUS
Density % sol: 70.5 %
Crystal grow
*PLUS
pH: 7.3 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
15 %(w/v)PEG1reservoir
210 mM1reservoirCaCl2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX9.6 / Wavelength: 0.876
DetectorType: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Oct 11, 1994
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.876 Å / Relative weight: 1
ReflectionResolution: 2.5→42.2 Å / Num. obs: 22212 / % possible obs: 94.2 % / Redundancy: 3.27 % / Rmerge(I) obs: 0.086
Reflection
*PLUS
Num. measured all: 72655 / Rmerge(I) obs: 0.086
Reflection shell
*PLUS
% possible obs: 66.7 % / Rmerge(I) obs: 0.23

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
X-PLOR3.1model building
X-PLOR3.1refinement
X-PLOR3.1phasing
RefinementResolution: 2.5→9 Å / σ(F): 0
Details: THE CONFORMATION OF THE MAIN CHAIN IS NOT WELL DEFINED FOR RESIDUES 263 - 268, 306 - 311 AND 402 - 409.
RfactorNum. reflection% reflection
Rwork0.217 --
obs0.217 21539 94.3 %
Displacement parametersBiso mean: 34.3 Å2
Refinement stepCycle: LAST / Resolution: 2.5→9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2966 0 33 295 3294
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.015
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.92
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d26.3
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.75
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it1.5
X-RAY DIFFRACTIONx_mcangle_it2
X-RAY DIFFRACTIONx_scbond_it2
X-RAY DIFFRACTIONx_scangle_it2.5
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg26.3
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.75
LS refinement shell
*PLUS
Highest resolution: 2.5 Å / Lowest resolution: 2.61 Å / Rfactor obs: 0.366

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