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- PDB-3shi: Crystal structure of human MMP1 catalytic domain at 2.2 A resolution -

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Basic information

Entry
Database: PDB / ID: 3shi
TitleCrystal structure of human MMP1 catalytic domain at 2.2 A resolution
ComponentsInterstitial collagenase
KeywordsHYDROLASE / matrix metalloproteinase / paramagnetic restraints / paramagnetic tag / lanthanides / protein refinement / residual dipolar couplings
Function / homology
Function and homology information


interstitial collagenase / cellular response to UV-A / protein metabolic process / Basigin interactions / Activation of Matrix Metalloproteinases / Collagen degradation / collagen catabolic process / extracellular matrix disassembly / Degradation of the extracellular matrix / extracellular matrix organization ...interstitial collagenase / cellular response to UV-A / protein metabolic process / Basigin interactions / Activation of Matrix Metalloproteinases / Collagen degradation / collagen catabolic process / extracellular matrix disassembly / Degradation of the extracellular matrix / extracellular matrix organization / extracellular matrix / positive regulation of protein-containing complex assembly / metalloendopeptidase activity / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / peptidase activity / Interleukin-4 and Interleukin-13 signaling / endopeptidase activity / serine-type endopeptidase activity / proteolysis / extracellular space / zinc ion binding / extracellular region
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
Interstitial collagenase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsBertini, I. / Calderone, V. / Cerofolini, L. / Fragai, M. / Geraldes, C.F.G.C. / Hermann, P. / Luchinat, C. / Parigi, G. / Teixeira, J.
Citation
Journal: Febs Lett. / Year: 2012
Title: The catalytic domain of MMP-1 studied through tagged lanthanides.
Authors: Bertini, I. / Calderone, V. / Cerofolini, L. / Fragai, M. / Geraldes, C.F. / Hermann, P. / Luchinat, C. / Parigi, G. / Teixeira, J.M.
#1: Journal: Biochemistry / Year: 1994
Title: Crystal structures of recombinant 19-kDa human fibroblast collagenase complexed to itself.
Authors: Lovejoy, B. / Hassell, A.M. / Luther, M.A. / Weigl, D. / Jordan, S.R.
#2: Journal: Proteins / Year: 1994
Title: 1.56 A structure of mature truncated human fibroblast collagenase.
Authors: Spurlino, J.C. / Smallwood, A.M. / Carlton, D.D. / Banks, T.M. / Vavra, K.J. / Johnson, J.S. / Cook, E.R. / Falvo, J. / Wahl, R.C. / Pulvino, T.A.
#3: 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. / Hendricks, R.T. / Campbell, J.A. / Walker, K.A. / Martin, R. / Van Wart, H. / Browner, M.F.
History
DepositionJun 16, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 21, 2011Provider: repository / Type: Initial release
Revision 1.1Oct 12, 2011Group: Database references
Revision 1.2Mar 21, 2012Group: Database references
Revision 1.3Nov 8, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Sep 13, 2023Group: 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 / 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_asym_id / _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_asym_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_asym_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_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_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: Interstitial collagenase
G: Interstitial collagenase
M: Interstitial collagenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,12718
Polymers52,3743
Non-polymers75315
Water5,423301
1
A: Interstitial collagenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,7096
Polymers17,4581
Non-polymers2515
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
G: Interstitial collagenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,7096
Polymers17,4581
Non-polymers2515
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
M: Interstitial collagenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,7096
Polymers17,4581
Non-polymers2515
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)147.694, 54.528, 94.905
Angle α, β, γ (deg.)90.00, 120.69, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-3-

HOH

21G-21-

HOH

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Components

#1: Protein Interstitial collagenase / MMP-1 / Matrix metalloproteinase-1 / 22 kDa interstitial collagenase / Fibroblast collagenase


Mass: 17457.984 Da / Num. of mol.: 3 / Fragment: UNP residues 106-261
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MMP1, CLG / Production host: Escherichia coli (E. coli) / References: UniProt: P03956, interstitial collagenase
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 301 / 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: 3.13 Å3/Da / Density % sol: 60.67 %
Crystal growpH: 8.5 / Details: 30% PEG8000, 0.1 M Tris-HCl, pH 8.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SEALED TUBE / Type: OXFORD DIFFRACTION ENHANCE ULTRA / Wavelength: 1.5406
DetectorType: OXFORD ONYX CCD / Detector: CCD / Date: Jul 26, 2005 / Details: mirrors
RadiationMonochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5406 Å / Relative weight: 1
ReflectionResolution: 2.2→81.65 Å / Num. all: 32923 / Num. obs: 32923 / % possible obs: 99.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3 % / Biso Wilson estimate: 40.1 Å2 / Rmerge(I) obs: 0.066 / Rsym value: 0.066 / Net I/σ(I): 9.1
Reflection shellResolution: 2.2→2.32 Å / Redundancy: 3 % / Rmerge(I) obs: 0.49 / Mean I/σ(I) obs: 1.8 / Rsym value: 0.49 / % possible all: 99.8

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Processing

Software
NameVersionClassification
CrysalisProdata collection
MOLREPphasing
REFMAC5.6.0109refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 966C

966c


Resolution: 2.2→81.65 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.901 / Isotropic thermal model: ISOTROPIC, / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.258 / ESU R Free: 0.233 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.27814 2988 9.1 %RANDOM
Rwork0.20898 ---
all0.21528 29931 --
obs0.21528 29931 98.87 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 38.576 Å2
Baniso -1Baniso -2Baniso -3
1--0.43 Å20 Å2-1.05 Å2
2--0.69 Å20 Å2
3----1.34 Å2
Refinement stepCycle: LAST / Resolution: 2.2→81.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3708 0 15 301 4024
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.0213831
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.0211.9185217
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.8815465
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.02723.973219
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.32515549
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.0561527
X-RAY DIFFRACTIONr_chiral_restr0.1870.2525
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0213135
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.368 223 -
Rwork0.282 2212 -
obs--99.67 %

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