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- PDB-6hv2: MMP-13 in complex with the peptide IMISF -

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Basic information

Entry
Database: PDB / ID: 6hv2
TitleMMP-13 in complex with the peptide IMISF
Components(Collagenase 3) x 2
KeywordsMETAL BINDING PROTEIN / peptidase / matrix metallo protease / self-degradation / MMP
Function / homology
Function and homology information


growth plate cartilage development / RUNX2 regulates genes involved in cell migration / endochondral ossification / Hydrolases; Acting on peptide bonds (peptidases); Metalloendopeptidases / bone morphogenesis / Assembly of collagen fibrils and other multimeric structures / bone mineralization / Activation of Matrix Metalloproteinases / response to amyloid-beta / Collagen degradation ...growth plate cartilage development / RUNX2 regulates genes involved in cell migration / endochondral ossification / Hydrolases; Acting on peptide bonds (peptidases); Metalloendopeptidases / bone morphogenesis / Assembly of collagen fibrils and other multimeric structures / bone mineralization / Activation of Matrix Metalloproteinases / response to amyloid-beta / Collagen degradation / collagen catabolic process / extracellular matrix disassembly / collagen binding / Degradation of the extracellular matrix / extracellular matrix organization / extracellular matrix / metalloendopeptidase activity / endopeptidase activity / serine-type endopeptidase activity / calcium ion binding / 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
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.709 Å
AuthorsMittl, P. / Riedl, R. / Hohl, D.
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2019
Title: Drug Design Inspired by Nature: Crystallographic Detection of an Auto-Tailored Protease Inhibitor Template.
Authors: Gall, F.M. / Hohl, D. / Frasson, D. / Wermelinger, T. / Mittl, P.R.E. / Sievers, M. / Riedl, R.
History
DepositionOct 10, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 30, 2019Provider: repository / Type: Initial release
Revision 1.1Feb 13, 2019Group: Data collection / Database references / Category: citation / citation_author / pdbx_database_proc / Item: _citation.title / _citation_author.identifier_ORCID
Revision 1.2Mar 20, 2019Group: Data collection / Database references / Category: citation / citation_author / pdbx_database_proc
Item: _citation.journal_abbrev / _citation.journal_volume ..._citation.journal_abbrev / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Apr 22, 2020Group: Database references / Category: pdbx_related_exp_data_set
Revision 1.4Jan 24, 2024Group: 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 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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_conn.ptnr2_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Collagenase 3
B: Collagenase 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,8628
Polymers19,5192
Non-polymers3436
Water1,38777
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1360 Å2
ΔGint-69 kcal/mol
Surface area8710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.928, 68.928, 133.563
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122
Components on special symmetry positions
IDModelComponents
11B-201-

HOH

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Components

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Protein / Protein/peptide , 2 types, 2 molecules AB

#1: Protein Collagenase 3 / Matrix metalloproteinase-13 / MMP-13


Mass: 18909.076 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MMP13 / Production host: Escherichia coli (E. coli)
References: UniProt: P45452, Hydrolases; Acting on peptide bonds (peptidases); Metalloendopeptidases
#2: Protein/peptide Collagenase 3 / Matrix metalloproteinase-13 / MMP-13


Mass: 609.778 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: auto-proteolytic fragment of MMP-13 / Source: (gene. exp.) Homo sapiens (human) / Gene: MMP13 / Production host: Escherichia coli (E. coli)
References: UniProt: P45452, Hydrolases; Acting on peptide bonds (peptidases); Metalloendopeptidases

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Non-polymers , 4 types, 83 molecules

#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 77 / 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: 2.35 Å3/Da / Density % sol: 47.58 %
Crystal growTemperature: 293 K / Method: vapor diffusion
Details: 50 mM glycine, 20% PEG4000, 1 M ammonium formate, pH 9.4
PH range: 8.0 - 9.4

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.99987 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 14, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99987 Å / Relative weight: 1
ReflectionResolution: 1.709→34.46 Å / Num. obs: 21019 / % possible obs: 99.68 % / Redundancy: 37.3 % / Biso Wilson estimate: 31.52 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.2106 / Rrim(I) all: 0.2136 / Net I/σ(I): 18.59
Reflection shellResolution: 1.709→1.77 Å / Redundancy: 36.5 % / Mean I/σ(I) obs: 1.31 / Num. unique obs: 2003 / CC1/2: 0.634 / % possible all: 97.85

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Processing

Software
NameVersionClassification
PHENIX(1.14_3260: ???)refinement
XDSVERSION May 1, 2016 BUILT=20160617data reduction
XDSVERSION May 1, 2016 BUILT=20160617data scaling
MOLREPVers 11.4.06phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2ow9

2ow9


Resolution: 1.709→34.46 Å / SU ML: 0.31 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 37.23
RfactorNum. reflection% reflection
Rfree0.263 1942 5.07 %
Rwork0.2138 --
obs0.2163 21000 99.64 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.709→34.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1356 0 11 77 1444
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0051435
X-RAY DIFFRACTIONf_angle_d0.6491948
X-RAY DIFFRACTIONf_dihedral_angle_d12.461820
X-RAY DIFFRACTIONf_chiral_restr0.045196
X-RAY DIFFRACTIONf_plane_restr0.005252
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7092-1.75190.44921360.44622533X-RAY DIFFRACTION97
1.7519-1.79930.42161380.41442584X-RAY DIFFRACTION100
1.7993-1.85220.47431350.38862618X-RAY DIFFRACTION100
1.8522-1.9120.37361410.36132614X-RAY DIFFRACTION100
1.912-1.98030.37461410.32812603X-RAY DIFFRACTION100
1.9803-2.05960.36851310.31782614X-RAY DIFFRACTION100
2.0596-2.15340.35131360.31562599X-RAY DIFFRACTION100
2.1534-2.26690.33631420.3112581X-RAY DIFFRACTION100
2.2669-2.40890.39031400.30672583X-RAY DIFFRACTION100
2.4089-2.59480.29651370.25872616X-RAY DIFFRACTION100
2.5948-2.85580.24651400.20132594X-RAY DIFFRACTION100
2.8558-3.26880.22161370.17752628X-RAY DIFFRACTION100
3.2688-4.11740.21361400.15362589X-RAY DIFFRACTION100
4.1174-35.69590.2071480.14932612X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 32.592 Å / Origin y: -6.6922 Å / Origin z: 16.4356 Å
111213212223313233
T0.2452 Å20.0056 Å20.0473 Å2-0.4003 Å20.0319 Å2--0.2619 Å2
L1.957 °2-0.755 °20.7046 °2-3.0523 °2-0.5954 °2--3.8039 °2
S-0.1982 Å °-0.2247 Å °0.0522 Å °0.3403 Å °0.3091 Å °0.2314 Å °-0.4281 Å °-0.5188 Å °-0.0747 Å °
Refinement TLS groupSelection details: all

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