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- PDB-4rbm: Porphyromonas gingivalis gingipain K (Kgp) catalytic and immunogl... -

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Basic information

Entry
Database: PDB / ID: 4rbm
TitlePorphyromonas gingivalis gingipain K (Kgp) catalytic and immunoglobulin superfamily-like domains
ComponentsLys-gingipain W83
KeywordsHYDROLASE / alpha/beta-hydrolase / cysteine peptidase / lysine-containing substrates / extracellular / secreted
Function / homology
Function and homology information


gingipain K / hemolysis in another organism / cysteine-type endopeptidase activity / calcium ion binding / proteolysis / extracellular region
Similarity search - Function
Cleaved adhesin / Peptidase C25, gingipain, C-terminal / Cleaved Adhesin Domain / Domain of unknown function (DUF2436) / Peptidase C25, Ig-like domain / Gingipain propeptide / Gingipain propeptide superfamily / Gingipain, N-terminal / Peptidase family C25, C terminal ig-like domain / Propeptide_C25 ...Cleaved adhesin / Peptidase C25, gingipain, C-terminal / Cleaved Adhesin Domain / Domain of unknown function (DUF2436) / Peptidase C25, Ig-like domain / Gingipain propeptide / Gingipain propeptide superfamily / Gingipain, N-terminal / Peptidase family C25, C terminal ig-like domain / Propeptide_C25 / Gingipain / Gingipain, N-terminal superfamily / Peptidase family C25 / Caspase-like domain superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
ACETATE ION / AZIDE ION / (3S)-3,7-diaminoheptan-2-one / HISTIDINE / NICKEL (II) ION / Lys-gingipain W83
Similarity search - Component
Biological speciesPorphyromonas gingivalis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
Authorsde Diego, I. / Veillard, F. / Sztukowska, M.N. / Guevara, T. / Potempa, B. / Pomowski, A. / Huntington, J.A. / Potempa, J. / Gomis-Ruth, F.X.
CitationJournal: J.Biol.Chem. / Year: 2014
Title: Structure and Mechanism of Cysteine Peptidase Gingipain K (Kgp), a Major Virulence Factor of Porphyromonas gingivalis in Periodontitis.
Authors: de Diego, I. / Veillard, F. / Sztukowska, M.N. / Guevara, T. / Potempa, B. / Pomowski, A. / Huntington, J.A. / Potempa, J. / Gomis-Ruth, F.X.
History
DepositionSep 12, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 8, 2014Provider: repository / Type: Initial release
Revision 1.1Oct 15, 2014Group: Database references
Revision 1.2Dec 10, 2014Group: Database references
Revision 1.3Nov 22, 2017Group: Refinement description / Category: software
Revision 1.4Sep 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_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_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_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_leaving_atom_flag / _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_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
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection / Derived calculations
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp_atom / chem_comp_bond / struct_conn
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_label_atom_id / _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_1 / _chem_comp_bond.atom_id_2 / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Lys-gingipain W83
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,13418
Polymers51,0131
Non-polymers1,12117
Water9,602533
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)56.640, 58.810, 135.500
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Lys-gingipain W83 / Lysine specific cysteine protease / Lysine-specific cysteine proteinase / Porphypain / PrtK48 / Lys- ...Lysine specific cysteine protease / Lysine-specific cysteine proteinase / Porphypain / PrtK48 / Lys-gingipain catalytic subunit / 39 kDa adhesin / PrtK39 / 15 kDa adhesin / PrtK15 / 44 kDa adhesin / PrtK44


Mass: 51012.785 Da / Num. of mol.: 1 / Fragment: UNP residues 229-683
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Porphyromonas gingivalis (bacteria) / Gene: kgp, prtK, prtP / Production host: Escherichia coli (E. coli) / References: UniProt: Q51817, gingipain K

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Non-polymers , 9 types, 550 molecules

#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ni
#5: Chemical ChemComp-HIS / HISTIDINE


Type: L-peptide linking / Mass: 156.162 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H10N3O2
#6: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#7: Chemical ChemComp-AZI / AZIDE ION


Mass: 42.020 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: N3
#8: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#9: Chemical ChemComp-CKC / (3S)-3,7-diaminoheptan-2-one


Mass: 144.215 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H16N2O
#10: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 533 / 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: 2.21 Å3/Da / Density % sol: 44.39 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: The best crystals were obtained at 20C with protein solution (at 5.7mg/mL in 5mM Tris HCl, pH 7.4, 0.02% sodium azide) and 22% polyethylene glycol 8000, 0.1M sodium cacodylate, pH 6.5, 0.2M ...Details: The best crystals were obtained at 20C with protein solution (at 5.7mg/mL in 5mM Tris HCl, pH 7.4, 0.02% sodium azide) and 22% polyethylene glycol 8000, 0.1M sodium cacodylate, pH 6.5, 0.2M calcium acetate as reservoir solution from 2:1 uL drops, 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, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9393 Å / Relative weight: 1
ReflectionResolution: 1.75→45.2 Å / Num. all: 46542 / Num. obs: 46309 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.6 % / Biso Wilson estimate: 22 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 16.5
Reflection shellResolution: 1.75→1.79 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.692 / Mean I/σ(I) obs: 1.9 / Num. unique all: 3192 / % possible all: 93.9

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
BUSTER2.11.5refinement
XDSdata reduction
XDSdata scaling
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1CVR

1cvr


Resolution: 1.75→44.41 Å / Cor.coef. Fo:Fc: 0.9631 / Cor.coef. Fo:Fc free: 0.9554 / SU R Cruickshank DPI: 0.097 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.1722 767 1.66 %RANDOM
Rwork0.1492 ---
obs0.1496 46299 99.56 %-
all-46504 --
Displacement parametersBiso mean: 18.99 Å2
Baniso -1Baniso -2Baniso -3
1-0.8105 Å20 Å20 Å2
2---0.5876 Å20 Å2
3----0.2229 Å2
Refine analyzeLuzzati coordinate error obs: 0.162 Å
Refinement stepCycle: LAST / Resolution: 1.75→44.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3520 0 67 533 4120
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.013672HARMONIC2
X-RAY DIFFRACTIONt_angle_deg14988HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1602SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes81HARMONIC2
X-RAY DIFFRACTIONt_gen_planes533HARMONIC5
X-RAY DIFFRACTIONt_it3672HARMONIC20
X-RAY DIFFRACTIONt_nbd22SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion4.49
X-RAY DIFFRACTIONt_other_torsion2.55
X-RAY DIFFRACTIONt_chiral_improper_torsion474SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact4210SEMIHARMONIC4
LS refinement shellResolution: 1.75→1.79 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2485 47 1.46 %
Rwork0.2202 3166 -
all0.2206 3213 -
obs-3213 99.56 %
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)
10.49590.0138-0.07250.1857-0.00850.3452-0.0217-0.02070.0014-0.00970.0087-0.00030.0109-0.00220.013-0.03480.002-0.0007-0.0148-0.0075-0.036435.020542.41919.785
27.12272.15772.09241.93540.32042.4156-0.51620.23750.9871-0.29090.10.0395-0.55190.22170.41610.1457-0.0394-0.0723-0.03310.03220.197543.3569.395810.0328
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|229 - A|600 }A229 - 600
2X-RAY DIFFRACTION2{ A|601 - A|680 }A601 - 680

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