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- PDB-4itc: Crystal Structure Analysis of the K1 Cleaved Adhesin domain of Ly... -

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Basic information

Entry
Database: PDB / ID: 4itc
TitleCrystal Structure Analysis of the K1 Cleaved Adhesin domain of Lys-gingipain (Kgp) from Porphyromonas gingivalis W83
ComponentsLys-gingipain W83
KeywordsHYDROLASE / beta sandwich / cleaved adhesin family / lys-gingipain / hemagglutinin domain / cell invasion / Cysteine Protease / Calcium Binding / Membrane surface
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 / Jelly Rolls - #200 / Jelly Rolls / Immunoglobulin-like fold / Sandwich / Mainly Beta
Similarity search - Domain/homology
GUANIDINE / Lys-gingipain W83
Similarity search - Component
Biological speciesPorphyromonas gingivalis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.55 Å
AuthorsGanuelas, L.A. / Li, N. / Hunter, N. / Collyer, C.A.
CitationJournal: Eur J Microbiol Immunol (Bp) / Year: 2013
Title: The lysine gingipain adhesin domains from Porphyromonas gingivalis interact with erythrocytes and albumin: Structures correlate to function.
Authors: Ganuelas, L.A. / Li, N. / Yun, P. / Hunter, N. / Collyer, C.A.
History
DepositionJan 18, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 25, 2013Provider: repository / Type: Initial release
Revision 1.1Jan 15, 2014Group: Database references
Revision 1.2Nov 15, 2017Group: Refinement description / Category: software
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_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_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_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_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

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Assembly

Deposited unit
A: Lys-gingipain W83
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,9918
Polymers18,5491
Non-polymers4427
Water2,216123
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)34.034, 33.321, 67.245
Angle α, β, γ (deg.)90.000, 93.960, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#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: 18549.400 Da / Num. of mol.: 1 / Fragment: K1 Cleaved Adhesin Domain, residues 982-1154
Source method: isolated from a genetically manipulated source
Details: GST tag removed / Source: (gene. exp.) Porphyromonas gingivalis (bacteria) / Strain: W83 / Gene: kgp, prtK, prtP / Plasmid: pGEX-5X-3 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q51817, gingipain K
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-GAI / GUANIDINE / Guanidine


Mass: 59.070 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: CH5N3
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 123 / 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: 2.05 Å3/Da / Density % sol: 40.02 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.6
Details: 40 mM KH2PO4, 20% (v/v) glycerol, 16% (w/v) PEG 8000, 1 M guanidine hydrochloride, pH 7.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 8, 2011
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.55→50 Å / Num. all: 22038 / Num. obs: 22016 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 4.7 % / Biso Wilson estimate: 20.9 Å2 / Rmerge(I) obs: 0.06 / Χ2: 1.001 / Net I/σ(I): 13.6
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allΧ2% possible all
1.55-1.614.70.3424.17321731.015100
1.61-1.674.70.2765.02721810.978100
1.67-1.754.70.2186.85721841.01100
1.75-1.844.80.1628.57721760.986100
1.84-1.954.80.12112.02321931.044100
1.95-2.14.80.10212.02422040.93399.8
2.1-2.324.80.08915.22421740.97499.9
2.32-2.654.70.06221.53422271.03999.9
2.65-3.344.70.03634.33622271.02100
3.34-504.80.02745.92522771.01299.6

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 44.47 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.6 Å33.13 Å
Translation2.6 Å33.13 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASER2.1.4phasing
REFMACrefinement
PDB_EXTRACT3.11data extraction
Blu-Icedata collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3M1H

3m1h


Resolution: 1.55→24.74 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.953 / WRfactor Rfree: 0.1967 / WRfactor Rwork: 0.1681 / Occupancy max: 1 / Occupancy min: 0.3 / FOM work R set: 0.8973 / SU B: 1.254 / SU ML: 0.046 / SU R Cruickshank DPI: 0.0751 / SU Rfree: 0.0756 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.075 / ESU R Free: 0.076 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: Conjugate gradient method
RfactorNum. reflection% reflectionSelection details
Rfree0.1814 1000 4.8 %RANDOM
Rwork0.1533 ---
obs0.1546 20886 99.25 %-
all-21043 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 45.51 Å2 / Biso mean: 14.3556 Å2 / Biso min: 6.27 Å2
Baniso -1Baniso -2Baniso -3
1-0.05 Å20 Å20.07 Å2
2---0 Å2-0 Å2
3----0.06 Å2
Refinement stepCycle: LAST / Resolution: 1.55→24.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1244 0 26 123 1393
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0191360
X-RAY DIFFRACTIONr_bond_other_d0.0010.021182
X-RAY DIFFRACTIONr_angle_refined_deg1.591.941863
X-RAY DIFFRACTIONr_angle_other_deg0.7832712
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.5465183
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.37525.25459
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.15615176
X-RAY DIFFRACTIONr_dihedral_angle_4_deg9.081153
X-RAY DIFFRACTIONr_chiral_restr0.1040.2199
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0211670
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02350
LS refinement shellResolution: 1.55→1.591 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.258 75 -
Rwork0.186 1466 -
all-1541 -
obs-1500 95.12 %

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