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- PDB-3km5: Crystal Structure Analysis of the K2 Cleaved Adhesin Domain of Ly... -

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Basic information

Entry
Database: PDB / ID: 3km5
TitleCrystal Structure Analysis of the K2 Cleaved Adhesin Domain of Lys-gingipain (Kgp)
ComponentsLysine specific cysteine protease
KeywordsCELL INVASION / beta jelly roll barrel / cleaved adhesin family / LYS-gingipain / hemagglutination domain
Function / homology
Function and homology information


gingipain K / hemolysis in another organism / : / cysteine-type peptidase activity / 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 / Fibronectin type 3 domain / Fibronectin type III / Jelly Rolls / Immunoglobulin-like fold / Sandwich / Mainly Beta
Similarity search - Domain/homology
NITRATE ION / Lys-gingipain W83 / Hemagglutinin A
Similarity search - Component
Biological speciesPorphyromonas gingivalis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.4 Å
AuthorsLi, N. / Collyer, C.A. / Hunter, N.
CitationJournal: Mol.Microbiol. / Year: 2010
Title: Structure determination and analysis of a haemolytic gingipain adhesin domain from Porphyromonas gingivalis
Authors: Li, N. / Yun, P. / Nadkarni, M.A. / Ghadikolaee, N.B. / Nguyen, K.-A. / Lee, M. / Hunter, N. / Collyer, C.A.
History
DepositionNov 9, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 31, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
Revision 1.3Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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_seq_id / _pdbx_struct_conn_angle.ptnr2_label_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_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_ref_seq_dif.details / _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: Lysine specific cysteine protease
B: Lysine specific cysteine protease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,24710
Polymers38,7742
Non-polymers4728
Water5,477304
1
A: Lysine specific cysteine protease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,6255
Polymers19,3871
Non-polymers2384
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Lysine specific cysteine protease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,6215
Polymers19,3871
Non-polymers2344
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)29.911, 59.858, 85.672
Angle α, β, γ (deg.)90.000, 94.230, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Lysine specific cysteine protease


Mass: 19387.150 Da / Num. of mol.: 2 / Fragment: K2 cleaved adhesin domain, residues 1157-1334
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Porphyromonas gingivalis (bacteria) / Strain: W83 / Gene: kgp / Plasmid: pET32 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O52050, UniProt: P59915*PLUS

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Non-polymers , 5 types, 312 molecules

#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-NO3 / NITRATE ION / Nitrate


Mass: 62.005 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: NO3
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 304 / 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: 2

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Sample preparation

CrystalDensity Matthews: 1.97 Å3/Da / Density % sol: 37.64 % / Mosaicity: 1.049 °
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: 2.0M Ammonium sulfate, 0.2M Ammonium nitrate, 0.1M Na citrate, pH 5.6, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONAustralian Synchrotron MX110.95667
SYNCHROTRONAPS 23-ID-B20.97949, 0.97962, 0.94947
Detector
TypeIDDetectorDate
ADSC QUANTUM 210r1CCDJul 15, 2008
MARMOSAIC 300 mm CCD2CCDFeb 24, 2008
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2MADMx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
10.956671
20.979491
30.979621
40.949471
ReflectionResolution: 1.4→17 Å / Num. obs: 56082 / % possible obs: 94.8 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.058 / Χ2: 0.998 / Net I/σ(I): 11.8
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
1.4-1.423.60.26628640.99396
1.42-1.453.60.25627811.00495.5
1.45-1.483.60.23527831.00494.8
1.48-1.513.60.21627710.99494.3
1.51-1.543.60.1927471.00693.6
1.54-1.583.60.16727890.99493.6
1.58-1.623.60.1526950.99393.1
1.62-1.663.50.13627801.00392.6
1.66-1.713.60.11827000.99692.6
1.71-1.763.50.10527450.99392.3
1.76-1.833.60.09926651.00891.8
1.83-1.93.50.08127340.99592
1.9-1.993.50.06827340.99892.1
1.99-2.093.50.0627410.99892.6
2.09-2.223.40.05727961.00194.7
2.22-2.393.40.05328730.99396.9
2.39-2.633.60.0529301.00699.1
2.63-3.013.80.04629911.00199.8
3.01-3.7940.04329670.98599.7
3.79-173.80.04229960.99898.2

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.5.0063refinement
PDB_EXTRACT3.005data extraction
Blu-Icedata collection
HKL-2000data reduction
HKL-2000data scaling
SHELXCDphasing
SHELXEmodel building
RefinementMethod to determine structure: MAD / Resolution: 1.4→15.32 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.937 / Occupancy max: 1 / Occupancy min: 0.4 / SU B: 1.041 / SU ML: 0.042 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.068 / ESU R Free: 0.072 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.208 2829 5 %RANDOM
Rwork0.175 ---
obs0.177 56068 94.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 44.59 Å2 / Biso mean: 14.589 Å2 / Biso min: 5.7 Å2
Baniso -1Baniso -2Baniso -3
1--0.67 Å20 Å2-0.06 Å2
2--0.79 Å20 Å2
3----0.12 Å2
Refinement stepCycle: LAST / Resolution: 1.4→15.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2646 0 23 304 2973
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0212756
X-RAY DIFFRACTIONr_bond_other_d0.0010.021726
X-RAY DIFFRACTIONr_angle_refined_deg1.4921.9243764
X-RAY DIFFRACTIONr_angle_other_deg0.86734209
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.9155359
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.25824.754122
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.14515378
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.482156
X-RAY DIFFRACTIONr_chiral_restr0.0910.2406
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.023186
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02586
X-RAY DIFFRACTIONr_mcbond_it1.77321749
X-RAY DIFFRACTIONr_mcbond_other0.6012732
X-RAY DIFFRACTIONr_mcangle_it2.46132778
X-RAY DIFFRACTIONr_scbond_it2.97941007
X-RAY DIFFRACTIONr_scangle_it4.0166981
LS refinement shellResolution: 1.401→1.437 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.261 183 -
Rwork0.208 3876 -
all-4059 -
obs--94.22 %

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