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- PDB-2xs3: Structure of karilysin catalytic MMP domain -

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Basic information

Entry
Database: PDB / ID: 2xs3
TitleStructure of karilysin catalytic MMP domain
Components
  • KARILYSIN PROTEASE
  • PEPTIDE ALA-PHE-THR-SER
KeywordsHYDROLASE / BACTERIAL MMP / VIRULENCE FACTOR / METALLOPROTEASE / ZINC-DEPENDENT / PEPTIDASE
Function / homology
Function and homology information


Hydrolases; Acting on peptide bonds (peptidases); Metalloendopeptidases / collagen catabolic process / extracellular matrix organization / 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)
SYNTHETIC CONSTRUCT (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsCerda-Costa, N. / Guevara, T. / Karim, A.Y. / Ksiazek, M. / Nguyen, K.-A. / Arolas, J.L. / Potempa, J. / Gomis-Ruth, F.X.
Citation
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.
#1: Journal: Biol.Chem. / Year: 2010
Title: A Novel Matrix Metalloprotease-Like Enzyme (Karilysin) of the Periodontal Pathogen Tannerella Forsythia Atcc 43037.
Authors: Karim, A.Y. / Kulczycka, M. / Kantyka, T. / Dubin, G. / Jabaiah, A. / Daugherty, P.S. / Thogersen, I.B. / Enghild, J.J. / Nguyen, K. / Potempa, J.
#2: Journal: J.Innate.Immun. / Year: 2010
Title: Proteolytic Inactivation of Ll-37 by Karilysin, a Novel Virulence Mechanism of Tannerella Forsythia.
Authors: Koziel, J. / Karim, A.Y. / Przybyszewska, K. / Ksiazek, M. / Rapala-Kozik, M. / Nguyen, K. / Potempa, J.
History
DepositionSep 24, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 3, 2010Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 15, 2019Group: Data collection / Experimental preparation / Other
Category: database_PDB_rev / database_PDB_rev_record ...database_PDB_rev / database_PDB_rev_record / exptl_crystal_grow / pdbx_database_proc / pdbx_database_status
Item: _exptl_crystal_grow.method / _exptl_crystal_grow.temp / _pdbx_database_status.recvd_author_approval
Revision 1.4Dec 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_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_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.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_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
C: PEPTIDE ALA-PHE-THR-SER
B: KARILYSIN PROTEASE
D: PEPTIDE ALA-PHE-THR-SER
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,6409
Polymers38,2564
Non-polymers3845
Water2,072115
1
A: KARILYSIN PROTEASE
C: PEPTIDE ALA-PHE-THR-SER
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,2594
Polymers19,1282
Non-polymers1312
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area950 Å2
ΔGint-43.8 kcal/mol
Surface area7740 Å2
MethodPISA
2
B: KARILYSIN PROTEASE
D: PEPTIDE ALA-PHE-THR-SER
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,3815
Polymers19,1282
Non-polymers2533
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1000 Å2
ΔGint-43.5 kcal/mol
Surface area8020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)121.370, 53.110, 86.300
Angle α, β, γ (deg.)90.00, 134.55, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein KARILYSIN PROTEASE / KARILYSIN CATALYTIC DOMAIN KLY18


Mass: 18703.615 Da / Num. of mol.: 2 / Fragment: 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 ALA-PHE-THR-SER


Mass: 424.448 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) SYNTHETIC CONSTRUCT (others)
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 115 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsZINC CATION (ZN): CATALYTIC 999 AND STRUCTURAL 998 ZINC IONS OF EACH OF THE TWO PROTEIN MOLECULES A AND B.
Sequence detailsONLY THE CATALYTIC DOMAIN (TYR35-PHE200) WAS CRYSTALLIZED. A PEPTIDE WAS FOUND AT THE ACTIVE SITE ...ONLY THE CATALYTIC DOMAIN (TYR35-PHE200) WAS CRYSTALLIZED. A PEPTIDE WAS FOUND AT THE ACTIVE SITE OF THE PROTEIN, WHICH HAS BEEN INTERPRETED AS ALA-PHE-THR-SER. AUTHOR SUGGESTS THAT THIS PEPTIDE MAY HAVE BEEN RECRUITED BY THE ENZYME DURING PROTEIN PRODUCTION/PURIFICATION/PROCESSING.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.54 Å3/Da / Density % sol: 51.51 % / Description: NONE
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: CRYSTALLIZATION ASSAYS WERE PERFORMED BY THE SITTING-DROP VAPOR DIFFUSION METHOD. RESERVOIR SOLUTIONS WERE PREPARED BY A TECAN ROBOT AND CRYSTALLIZATION DROPS WERE DISPENSED ON 96X2-WELL MRC ...Details: CRYSTALLIZATION ASSAYS WERE PERFORMED BY THE SITTING-DROP VAPOR DIFFUSION METHOD. RESERVOIR SOLUTIONS WERE PREPARED BY A TECAN ROBOT AND CRYSTALLIZATION DROPS WERE DISPENSED ON 96X2-WELL MRC PLATES (INNOVADYNE) BY A CARTESIAN (GENOMIC SOLUTIONS) NANODROP ROBOT AT THE HIGH-THROUGHPUT CRYSTALLOGRAPHY PLATFORM AT BARCELONA SCIENCE PARK. CRYSTALS SUITABLE FOR STRUCTURE ANALYSIS WERE OBTAINED FOR UNBOUND KLY18 IN A BRUKER STEADY-TEMPERATURE CRYSTAL FARM AT 20C FROM DROPS CONTAINING 100NL OF PROTEIN SOLUTION (AT 9MG ML-1 IN 5MM TRIS-HCL, PH8.0, 0.02% SODIUM AZIDE) AND 100NL OF 45% 2-METHYL-2,4-PENTANEDIOL, 0.2M AMMONIUM ACETATE, 0.1M TRIS-HCL, PH8.5 AS RESERVOIR SOLUTION.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8726
DetectorType: MARRESEARCH / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8726 Å / Relative weight: 1
ReflectionResolution: 2.4→45.3 Å / Num. obs: 15411 / % possible obs: 99.3 % / Observed criterion σ(I): 0 / Redundancy: 4.1 % / Biso Wilson estimate: 38.4 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 14.8
Reflection shellResolution: 2.4→2.53 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.51 / Mean I/σ(I) obs: 2.5 / % possible all: 95.9

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Processing

Software
NameVersionClassification
REFMAC5.5.0102refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1MNC

1mnc


Resolution: 2.4→50 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.897 / SU B: 17.868 / SU ML: 0.203 / Cross valid method: THROUGHOUT / ESU R: 0.422 / ESU R Free: 0.277 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.25872 708 4.6 %RANDOM
Rwork0.18877 ---
obs0.19197 14703 99.28 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 33.731 Å2
Baniso -1Baniso -2Baniso -3
1-3.2 Å20 Å22.49 Å2
2---1.7 Å20 Å2
3---1.99 Å2
Refinement stepCycle: LAST / Resolution: 2.4→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2702 0 12 115 2829
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0212795
X-RAY DIFFRACTIONr_bond_other_d0.0010.021803
X-RAY DIFFRACTIONr_angle_refined_deg1.3211.9193807
X-RAY DIFFRACTIONr_angle_other_deg0.88634380
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7295336
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.33224.348138
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.06415404
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.179156
X-RAY DIFFRACTIONr_chiral_restr0.0810.2390
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0213162
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02602
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_it0.6031.51682
X-RAY DIFFRACTIONr_mcbond_other0.1061.5694
X-RAY DIFFRACTIONr_mcangle_it1.10922688
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.4631113
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.2644.51119
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.4→2.462 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.485 50 -
Rwork0.283 1001 -
obs--92.84 %
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)
11.9317-0.2781-1.06153.02210.53053.78760.06830.25060.0213-0.3765-0.06670.1048-0.2003-0.3439-0.00150.05230.0147-0.01030.08760.01050.1037-26.12918.094-8.338
23.5364-0.13710.71453.7925-0.49561.94240.12770.31580.0836-0.1175-0.2118-0.31710.05750.24630.08410.07230.0087-0.00010.10030.01750.03047.93918.317-25.95
30.9331-0.1869-0.25190.7524-0.2430.75210.12080.2163-0.0417-0.1622-0.15920.0622-0.0727-0.03710.03840.1807-0.0024-0.04620.2306-0.03550.097-11.29417.07-18.275
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A35 - 200
2X-RAY DIFFRACTION1A999 - 998
3X-RAY DIFFRACTION2B35 - 200
4X-RAY DIFFRACTION2B999 - 998
5X-RAY DIFFRACTION3A301 - 304
6X-RAY DIFFRACTION3B301 - 304
7X-RAY DIFFRACTION3B1305

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