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- PDB-4auo: Crystal structure of MMP-1(E200A) in complex with a triple-helica... -

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Basic information

Entry
Database: PDB / ID: 4auo
TitleCrystal structure of MMP-1(E200A) in complex with a triple-helical collagen peptide
Components
  • INTERSTITIAL COLLAGENASE
  • TRIPLE-HELICAL COLLAGEN PEPTIDE
KeywordsHYDROLASE/PEPTIDE / HYDROLASE-PEPTIDE COMPLEX
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
4 Propeller / Hemopexin / Hemopexin-like domain / 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 ...4 Propeller / Hemopexin / Hemopexin-like domain / 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 / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Interstitial collagenase
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
SYNTHETIC CONSTRUCT (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsManka, S.W. / Carafoli, F. / Visse, R. / Bihan, D. / Raynal, N. / Farndale, R.W. / Murphy, G. / Enghild, J.J. / Hohenester, E. / Nagase, H.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2012
Title: Structural Insights Into Triple-Helical Collagen Cleavage by Matrix Metalloproteinase 1
Authors: Manka, S.W. / Carafoli, F. / Visse, R. / Bihan, D. / Raynal, N. / Farndale, R.W. / Murphy, G. / Enghild, J.J. / Hohenester, E. / Nagase, H.
History
DepositionMay 18, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 11, 2012Provider: repository / Type: Initial release
Revision 1.1Aug 15, 2012Group: Database references
Revision 1.2Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_conn_type / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_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_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.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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 / _struct_conn_type.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: INTERSTITIAL COLLAGENASE
B: INTERSTITIAL COLLAGENASE
C: TRIPLE-HELICAL COLLAGEN PEPTIDE
D: TRIPLE-HELICAL COLLAGEN PEPTIDE
E: TRIPLE-HELICAL COLLAGEN PEPTIDE
F: TRIPLE-HELICAL COLLAGEN PEPTIDE
G: TRIPLE-HELICAL COLLAGEN PEPTIDE
H: TRIPLE-HELICAL COLLAGEN PEPTIDE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)107,74120
Polymers107,1598
Non-polymers58212
Water1267
1
A: INTERSTITIAL COLLAGENASE
C: TRIPLE-HELICAL COLLAGEN PEPTIDE
D: TRIPLE-HELICAL COLLAGEN PEPTIDE
E: TRIPLE-HELICAL COLLAGEN PEPTIDE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,87110
Polymers53,5794
Non-polymers2916
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9870 Å2
ΔGint-106.3 kcal/mol
Surface area21230 Å2
MethodPISA
2
B: INTERSTITIAL COLLAGENASE
F: TRIPLE-HELICAL COLLAGEN PEPTIDE
G: TRIPLE-HELICAL COLLAGEN PEPTIDE
H: TRIPLE-HELICAL COLLAGEN PEPTIDE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,87110
Polymers53,5794
Non-polymers2916
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9580 Å2
ΔGint-101 kcal/mol
Surface area21050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.671, 102.241, 80.734
Angle α, β, γ (deg.)90.00, 103.75, 90.00
Int Tables number3
Space group name H-MP121

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Components

#1: Protein INTERSTITIAL COLLAGENASE / FIBROBLAST COLLAGENASE / MATRIX METALLOPROTEINASE-1 / MMP-1 / 22 KDA INTERSTITIAL COLLAGENASE / 27 ...FIBROBLAST COLLAGENASE / MATRIX METALLOPROTEINASE-1 / MMP-1 / 22 KDA INTERSTITIAL COLLAGENASE / 27 KDA INTERSTITIAL COLLAGENASE


Mass: 42230.070 Da / Num. of mol.: 2 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P03956, interstitial collagenase
#2: Protein/peptide
TRIPLE-HELICAL COLLAGEN PEPTIDE


Mass: 3783.110 Da / Num. of mol.: 6 / Source method: obtained synthetically / Source: (synth.) SYNTHETIC CONSTRUCT (others)
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Ca
#4: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 7 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN A, GLU 219 TO ALA ENGINEERED RESIDUE IN CHAIN B, GLU 219 TO ALA
Sequence detailsTHE CRYSTALLISED PROTEIN HAS A E200A MUTATION THAT RENDERS IT CATALYTICALLY INACTIVE

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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: 2.87 Å3/Da / Density % sol: 57.12 % / Description: NONE
Crystal growpH: 8 / Details: pH 8

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9778
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 13, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9778 Å / Relative weight: 1
ReflectionResolution: 3→20 Å / Num. obs: 20982 / % possible obs: 86.8 % / Observed criterion σ(I): 0 / Redundancy: 1.7 % / Rmerge(I) obs: 0.13 / Net I/σ(I): 5
Reflection shellResolution: 3→3.16 Å / Redundancy: 1.6 % / Rmerge(I) obs: 0.4 / Mean I/σ(I) obs: 2.2 / % possible all: 77.9

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Processing

Software
NameVersionClassification
CNS1.3refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2CLT

2clt


Resolution: 3→20 Å / Data cutoff high absF: 10000 / Data cutoff low absF: 0 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: THERE ARE TWO COMPLEXES IN THE ASYMMETRIC UNIT (CHAINS ACDE AND BFGH). THEY DIFFER ONLY IN THE ENDS OF THE COLLAGEN MOLECULES.
RfactorNum. reflection% reflectionSelection details
Rfree0.2727 2069 8.5 %RANDOM
Rwork0.2111 ---
obs0.2111 20982 86 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 13.979 Å2 / ksol: 0.35 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--14.887 Å20 Å20.709 Å2
2---0.414 Å20 Å2
3---15.301 Å2
Refinement stepCycle: LAST / Resolution: 3→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7368 0 12 7 7387
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
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_deg1.4
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1PROTEIN_REP-HYP.PARAM
X-RAY DIFFRACTION2ION.PARAM
X-RAY DIFFRACTION3WATER_REP.PARAM

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