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- PDB-4in9: Structure of karilysin MMP-like catalytic domain in complex with ... -

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Basic information

Entry
Database: PDB / ID: 4in9
TitleStructure of karilysin MMP-like catalytic domain in complex with inhibitory tetrapeptide SWFP
Components
  • Karilysin protease
  • Peptide SER-TRP-PHE-PRO
KeywordsHYDROLASE / matrixin / metallopeptidase / metalloprotease / hydrolytic enzyme
Function / homology
Function and homology information


Hydrolases; Acting on peptide bonds (peptidases); Metalloendopeptidases / collagen catabolic process / extracellular matrix organization / extracellular matrix / metalloendopeptidase activity / proteolysis / extracellular region / zinc ion binding
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)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.55 Å
AuthorsGuevara, T. / Ksiazek, M. / Skottrup, P.D. / Cerda-Costa, N. / Trillo-Muyo, S. / de Diego, I. / Riise, E. / Potempa, J. / Gomis-Ruth, F.X.
Citation
Journal: Acta Crystallogr.,Sect.F / Year: 2013
Title: Structure of the catalytic domain of the Tannerella forsythia matrix metallopeptidase karilysin in complex with a tetrapeptidic inhibitor.
Authors: Guevara, T. / Ksiazek, M. / Skottrup, P.D. / Cerda-Costa, N. / Trillo-Muyo, S. / de Diego, I. / Riise, E. / Potempa, J. / Gomis-Ruth, F.X.
#1: Journal: Mol.Microbiol. / Year: 2011
Title: The structure of the catalytic domain of Tannerella forsythia karilysin reveals it is a bacterial xenologue of animal matrix metalloproteinases.
Authors: Cerda-Costa, N. / Guevara, T. / Karim, A.Y. / Ksiazek, M. / Nguyen, K.A. / Arolas, J.L. / Potempa, J. / Gomis-Ruth, F.X.
History
DepositionJan 4, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 15, 2013Provider: repository / Type: Initial release
Revision 1.1Jun 19, 2013Group: Database references
Revision 1.2Nov 15, 2017Group: Refinement description / Source and taxonomy / Category: pdbx_entity_src_syn / software
Item: _pdbx_entity_src_syn.ncbi_taxonomy_id / _pdbx_entity_src_syn.organism_scientific
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_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_alt_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_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_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.pdbx_ptnr1_label_alt_id / _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_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 protease
B: Peptide SER-TRP-PHE-PRO
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,89311
Polymers19,2392
Non-polymers6539
Water3,747208
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2420 Å2
ΔGint-58 kcal/mol
Surface area7620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.050, 86.050, 49.440
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number79
Space group name H-MI4

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Components

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

#1: Protein Karilysin protease


Mass: 18703.615 Da / Num. of mol.: 1 / Fragment: UNP residues 35-200
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Tannerella forsythia (bacteria) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: D0EM77
#2: Protein/peptide Peptide SER-TRP-PHE-PRO


Mass: 535.591 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: Synthetic peptide arising from phage-display screening
Source: (synth.) synthetic construct (others)

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Non-polymers , 5 types, 217 molecules

#3: Chemical ChemComp-ZN / ZINC ION


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


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#6: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 18.015 Da / Num. of mol.: 208 / 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: 2.38 Å3/Da / Density % sol: 48.29 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8
Details: Best crystals were obtained at 20 degrees from 1:1 microL drops with complex solution (8mg/mL in 5mM Tris HCl pH8, 5mM calcium chloride, 0.02% sodium azide) and 0.4M sodium/potassium ...Details: Best crystals were obtained at 20 degrees from 1:1 microL drops with complex solution (8mg/mL in 5mM Tris HCl pH8, 5mM calcium chloride, 0.02% sodium azide) and 0.4M sodium/potassium tartrate as reservoir solution. Crystals were cryo-protected by immersion in cryo-solution (0.32M sodium/potassium tartrate, 25%[v/v] glycerol), VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9393 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 31, 2011
RadiationMonochromator: channel cut ESRF monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9393 Å / Relative weight: 1
ReflectionResolution: 1.55→42.9 Å / Num. all: 26370 / Num. obs: 26344 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 2 / Redundancy: 7 % / Biso Wilson estimate: 21.2 Å2 / Rmerge(I) obs: 0.081 / Net I/σ(I): 18.4
Reflection shellResolution: 1.55→1.59 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.749 / Mean I/σ(I) obs: 2.1 / % possible all: 98.7

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
BUSTER2.11.2refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 2XS4

2xs4


Resolution: 1.55→42.87 Å / Cor.coef. Fo:Fc: 0.9679 / Cor.coef. Fo:Fc free: 0.9567 / SU R Cruickshank DPI: 0.064 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.171 1335 5.07 %RANDOM
Rwork0.1453 ---
all0.1465 26370 --
obs0.1465 26318 99.9 %-
Displacement parametersBiso mean: 17.58 Å2
Baniso -1Baniso -2Baniso -3
1-0.5945 Å20 Å20 Å2
2--0.5945 Å20 Å2
3----1.1891 Å2
Refine analyzeLuzzati coordinate error obs: 0.137 Å
Refinement stepCycle: LAST / Resolution: 1.55→42.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1333 0 34 208 1575
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.011419HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.921924HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d0608SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes034HARMONIC2
X-RAY DIFFRACTIONt_gen_planes0199HARMONIC5
X-RAY DIFFRACTIONt_it01419HARMONIC20
X-RAY DIFFRACTIONt_nbd00SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion4.18
X-RAY DIFFRACTIONt_other_torsion2.7
X-RAY DIFFRACTIONt_chiral_improper_torsion0169SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies011HARMONIC1
X-RAY DIFFRACTIONt_ideal_dist_contact01813SEMIHARMONIC4
LS refinement shellResolution: 1.55→1.61 Å / Total num. of bins used: 13
RfactorNum. reflection% reflection
Rfree0.2107 159 5.45 %
Rwork0.2069 2760 -
all0.2071 2919 -
obs--99.92 %
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)
10.51420.00430.00920.4007-0.0310.5029-0.00280.01420.0283-0.0122-0.00470.0402-0.0545-0.00510.00750.0059-0.0038-0.00680.00180.0058-0.003198.9018109.458-15.621
20-0.57340.551200.20480.25190.0071-0.04130.03780.04710.0226-0.0543-0.11170.1037-0.02970.0259-0.0488-0.02140.0173-0.01240.0063111.49113.425-12.5512
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|35 - A|200 }A35 - 200
2X-RAY DIFFRACTION2{ B|1 - B|4 }B1 - 4

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