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- PDB-4r3v: Structure of karilysin propeptide and catalytic MMP domain -

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Basic information

Entry
Database: PDB / ID: 4r3v
TitleStructure of karilysin propeptide and catalytic MMP domain
ComponentsKarilysin
KeywordsHYDROLASE / Metzincin metallopeptidase / Matrix metalloproteinase with unique propeptide / Bacterial matrix metalloproteinase-like enzyme
Function / homology
Function and homology information


Hydrolases; Acting on peptide bonds (peptidases); Metalloendopeptidases / extracellular matrix / metalloendopeptidase activity / proteolysis / zinc ion binding / extracellular region
Similarity search - Function
Secretion system C-terminal sorting domain / Secretion system C-terminal sorting domain / Invasin/intimin cell-adhesion fragments / Peptidase M10A / Peptidase M10A, catalytic domain / Peptidase M10, metallopeptidase / Matrixin / Peptidase, metallopeptidase / Zinc-dependent metalloprotease / Collagenase (Catalytic Domain) ...Secretion system C-terminal sorting domain / Secretion system C-terminal sorting domain / Invasin/intimin cell-adhesion fragments / Peptidase M10A / Peptidase M10A, catalytic domain / Peptidase M10, metallopeptidase / Matrixin / 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 speciesTannerella forsythia (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.01 Å
AuthorsLopez-Pelegrin, M. / Ksiazek, M. / Karim, A.Y. / Guevara, T. / Arolas, J.L. / Potempa, J. / Gomis-Ruth, F.X.
CitationJournal: J.Biol.Chem. / Year: 2015
Title: A novel mechanism of latency in matrix metalloproteinases.
Authors: Lopez-Pelegrin, M. / Ksiazek, M. / Karim, A.Y. / Guevara, T. / Arolas, J.L. / Potempa, J. / Gomis-Ruth, F.X.
History
DepositionAug 18, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 7, 2015Provider: repository / Type: Initial release
Revision 1.1Jan 21, 2015Group: Database references
Revision 1.2Mar 11, 2015Group: Database references
Revision 1.3Sep 20, 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_ref_seq_dif / 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_ref_seq_dif.details / _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: Karilysin
B: Karilysin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,39511
Polymers40,7772
Non-polymers6189
Water4,071226
1
A: Karilysin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,8367
Polymers20,3881
Non-polymers4476
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Karilysin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,5594
Polymers20,3881
Non-polymers1713
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)36.180, 121.690, 41.880
Angle α, β, γ (deg.)90.00, 105.26, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Karilysin / Matrix metalloprotease-like enzyme / MMP-like enzyme / Karilysin long form Kly38 / Karilysin short form Kly18


Mass: 20388.416 Da / Num. of mol.: 2
Fragment: the propeptide and the catalytic domain (UNP residues 21-201)
Mutation: E156A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Tannerella forsythia (bacteria) / Strain: ATCC 43037 / JCM 10827 / FDC 338 / Gene: kly, BFO_2683 / Plasmid: pGEX-6P-1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: D0EM77, 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.: 2 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 226 / 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: 2.18 Å3/Da / Density % sol: 43.61 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1 M Bis-Tris propane, 0.2 M potassium thiocyanate, 20% (w/v) polyethylene glycol 3350, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.97242 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Nov 22, 2013
RadiationMonochromator: Si(311) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97242 Å / Relative weight: 1
ReflectionResolution: 2.01→60.8 Å / Num. all: 22975 / Num. obs: 22975 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 25.17 Å2 / Rmerge(I) obs: 0.105 / Net I/σ(I): 10.3
Reflection shellResolution: 2.01→2.11 Å / Rmerge(I) obs: 0.105 / Mean I/σ(I) obs: 10.3 / Num. unique all: 22975 / % possible all: 99.8

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Processing

Software
NameVersionClassification
MxCuBE(EDNA)data collection
PHASERphasing
BUSTER2.11.5refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 4IN9

4in9


Resolution: 2.01→60.8 Å / Cor.coef. Fo:Fc: 0.9394 / Cor.coef. Fo:Fc free: 0.9244 / SU R Cruickshank DPI: 0.182 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.194 741 3.25 %RANDOM
Rwork0.165 ---
obs0.165 22047 --
all-22047 --
Displacement parametersBiso mean: 30.81 Å2
Baniso -1Baniso -2Baniso -3
1-5.2342 Å20 Å2-7.8413 Å2
2---1.9049 Å20 Å2
3----3.3293 Å2
Refine analyzeLuzzati coordinate error obs: 0.215 Å
Refinement stepCycle: LAST / Resolution: 2.01→60.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2834 0 24 226 3084
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.012948HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.984020HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1273SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes76HARMONIC2
X-RAY DIFFRACTIONt_gen_planes432HARMONIC5
X-RAY DIFFRACTIONt_it2948HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion3.69
X-RAY DIFFRACTIONt_other_torsion2.81
X-RAY DIFFRACTIONt_chiral_improper_torsion370SEMIHARMONIC5
X-RAY DIFFRACTIONt_utility_distance28HARMONIC1
X-RAY DIFFRACTIONt_ideal_dist_contact3528SEMIHARMONIC4
LS refinement shellResolution: 2.01→2.11 Å / Total num. of bins used: 11
RfactorNum. reflection% reflection
Rfree0.194 741 3 %
Rwork0.165 2874 -
all0.1932 2963 -
obs-22047 -
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.5159-0.0086-0.16562.23020.30130.39850.02820.03610.1101-0.0631-0.0398-0.0719-0.0459-0.02490.0116-0.0307-0.005-0.0321-0.1117-0.00050.163123.46667.799814.9053
21.2783-0.1262-0.03511.30270.1870.26160.0334-0.02970.0495-0.0587-0.0199-0.0430.0224-0.0236-0.0134-0.063-0.0019-0.0552-0.1432-0.02230.196911.975736.925623.4357
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ B|21 - B|199 B|301 - B|301 B|302 - B|302 B|303 - B|303 }B21 - 199
2X-RAY DIFFRACTION1{ B|21 - B|199 B|301 - B|301 B|302 - B|302 B|303 - B|303 }B301
3X-RAY DIFFRACTION1{ B|21 - B|199 B|301 - B|301 B|302 - B|302 B|303 - B|303 }B302
4X-RAY DIFFRACTION1{ B|21 - B|199 B|301 - B|301 B|302 - B|302 B|303 - B|303 }B303
5X-RAY DIFFRACTION2{ A|21 - A|199 A|301 - A|301 A|302 - A|302 A|303 - A|303 }A21 - 199
6X-RAY DIFFRACTION2{ A|21 - A|199 A|301 - A|301 A|302 - A|302 A|303 - A|303 }A301
7X-RAY DIFFRACTION2{ A|21 - A|199 A|301 - A|301 A|302 - A|302 A|303 - A|303 }A302
8X-RAY DIFFRACTION2{ A|21 - A|199 A|301 - A|301 A|302 - A|302 A|303 - A|303 }A303

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