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- PDB-5mun: Structural insight into zymogenic latency of gingipain K from Por... -

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Basic information

Entry
Database: PDB / ID: 5mun
TitleStructural insight into zymogenic latency of gingipain K from Porphyromonas gingivalis.
ComponentsLys-gingipain W83
KeywordsHYDROLASE / Cysteine protease / zymogenic latency
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, N-terminal superfamily / Gingipain propeptide superfamily / Gingipain, N-terminal / Peptidase family C25, C terminal ig-like domain ...Cleaved adhesin / Peptidase C25, gingipain, C-terminal / Cleaved Adhesin Domain / Domain of unknown function (DUF2436) / Peptidase C25, Ig-like domain / Gingipain propeptide / Gingipain, N-terminal superfamily / Gingipain propeptide superfamily / Gingipain, N-terminal / Peptidase family C25, C terminal ig-like domain / Propeptide_C25 / Gingipain / Peptidase family C25 / Caspase-like domain superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
AZIDE ION / Lys-gingipain W83
Similarity search - Component
Biological speciesPorphyromonas gingivalis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 1.8 Å
AuthorsPomowski, A. / Uson, I. / Nowakovska, Z. / Veillard, F. / Sztukowska, M.N. / Guevara, T. / Goulas, T. / Mizgalska, D. / Nowak, M. / Potempa, B. ...Pomowski, A. / Uson, I. / Nowakovska, Z. / Veillard, F. / Sztukowska, M.N. / Guevara, T. / Goulas, T. / Mizgalska, D. / Nowak, M. / Potempa, B. / Huntington, J.A. / Potempa, J. / Gomis-Ruth, F.X.
Funding support Spain, Poland, 5items
OrganizationGrant numberCountry
European UnionFP7-HEALTH-2012-306029-2 TRIGGER Spain
Spanish Ministry of Economy and CompetitivenessBFU2015-64487R Spain
Ministry of Science and TechnologyBIO2013-49320-EXP Spain
Generalitat of Catalunya2014SGR9 Spain
Diamentowy Grant0218/DIA/2012/41 Poland
CitationJournal: J. Biol. Chem. / Year: 2017
Title: Structural insights unravel the zymogenic mechanism of the virulence factor gingipain K from Porphyromonas gingivalis, a causative agent of gum disease from the human oral microbiome.
Authors: Pomowski, A. / Uson, I. / Nowakowska, Z. / Veillard, F. / Sztukowska, M.N. / Guevara, T. / Goulas, T. / Mizgalska, D. / Nowak, M. / Potempa, B. / Huntington, J.A. / Potempa, J. / Gomis-Ruth, F.X.
History
DepositionJan 13, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 22, 2017Provider: repository / Type: Initial release
Revision 1.1Mar 1, 2017Group: Database references
Revision 1.2Apr 19, 2017Group: Database references
Revision 1.3Sep 13, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4May 8, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Lys-gingipain W83
B: Lys-gingipain W83
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,8933
Polymers46,8512
Non-polymers421
Water5,531307
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2380 Å2
ΔGint-12 kcal/mol
Surface area17830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.650, 66.250, 96.240
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Lys-gingipain W83 / Lysine specific cysteine protease / Lysine-specific cysteine proteinase / Porphypain / PrtK48


Mass: 23425.428 Da / Num. of mol.: 2 / Fragment: UNP residues 20-228
Source method: isolated from a genetically manipulated source
Details: The cloning strategy entailed that pentapeptide G-P-L-G-S from the expression vector was attached to the N-terminus of the recombinant protein.
Source: (gene. exp.) Porphyromonas gingivalis (bacteria) / Gene: kgp, prtK, prtP / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q51817, gingipain K
#2: Chemical ChemComp-AZI / AZIDE ION / Azide


Mass: 42.020 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: N3
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 307 / 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: 2.16 Å3/Da / Density % sol: 43.06 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 14 % polyvinylpyrrolidone K15 0.1 M Bis-Tris, pH 5.5

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Data collection

DiffractionMean temperature: 173.15 K
Ambient temp details: Data were collected from liquid-N2 flash-cryo-cooled crystals
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795, 1.8000
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Nov 7, 2012
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97951
21.81
ReflectionResolution: 1.8→96.2 Å / Num. obs: 38292 / % possible obs: 99.7 % / Redundancy: 4.4 % / Biso Wilson estimate: 33.5 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.054 / Rrim(I) all: 0.061 / Net I/σ(I): 19.8
Reflection shellResolution: 1.8→1.91 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.83 / Mean I/σ(I) obs: 1.95 / Num. unique obs: 6065 / CC1/2: 0.651 / Rrim(I) all: 0.943 / % possible all: 98.7

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
SHELXDEphasing
Cootmodel building
BUSTER2.10.2refinement
RefinementMethod to determine structure: SIRAS / Resolution: 1.8→25.75 Å / Cor.coef. Fo:Fc: 0.9537 / Cor.coef. Fo:Fc free: 0.9243 / SU R Cruickshank DPI: 0.122 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.13 / SU Rfree Blow DPI: 0.127 / SU Rfree Cruickshank DPI: 0.123
RfactorNum. reflection% reflectionSelection details
Rfree0.2404 742 1.94 %RANDOM
Rwork0.1969 ---
obs0.1978 38278 99.68 %-
Displacement parametersBiso mean: 37.15 Å2
Baniso -1Baniso -2Baniso -3
1--0.4286 Å20 Å20 Å2
2---0.3279 Å20 Å2
3---0.7565 Å2
Refine analyzeLuzzati coordinate error obs: 0.255 Å
Refinement stepCycle: 1 / Resolution: 1.8→25.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2758 0 3 307 3068
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.012817HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.13827HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1308SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes70HARMONIC2
X-RAY DIFFRACTIONt_gen_planes410HARMONIC5
X-RAY DIFFRACTIONt_it2817HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.69
X-RAY DIFFRACTIONt_other_torsion2.81
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion382SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies4HARMONIC1
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact3271SEMIHARMONIC4
LS refinement shellResolution: 1.8→1.85 Å / Total num. of bins used: 19
RfactorNum. reflection% reflection
Rfree0.2149 45 1.57 %
Rwork0.2617 2813 -
all0.261 2858 -
obs--97.43 %
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)
10.23740.2802-0.3381.6126-0.49170.9852-0.0157-0.05750.02170.00810.0092-0.1658-0.0173-0.00170.0065-0.0274-0.01310.0023-0.0109-0.01820.071734.068126.709816.2718
22.26651.1558-0.39812.937-0.39151.65480.1231-0.29780.20490.4835-0.08950.2089-0.11510.2513-0.03370.0785-0.0150.04160.0421-0.00770.049963.131933.69084.9094
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{A|20 - 201}
2X-RAY DIFFRACTION2{B|-2 - -1 B|20 - 199}

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