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- PDB-3m1h: Crystal Structure Analysis of the K3 Cleaved Adhesin Domain of Ly... -

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Basic information

Entry
Database: PDB / ID: 3m1h
TitleCrystal Structure Analysis of the K3 Cleaved Adhesin Domain of Lys-gingipain (Kgp) from Porphyromonas gingivalis w83
ComponentsLysine specific cysteine protease
KeywordsCELL INVASION / beta jelly roll barrel / cleaved adhesin family / lys-gingipain / hemagglutination domain / carbohydrate binding / Protease
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
Lys-gingipain W83 / Lys-gingipain W83
Similarity search - Component
Biological speciesPorphyromonas gingivalis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.56 Å
AuthorsLi, N. / Collyer, C.A. / Hunter, N.
Citation
Journal: Mol Microbiol / Year: 2011
Title: The modular structure of haemagglutinin/adhesin regions in gingipains of Porphyromonas gingivalis.
Authors: Nan Li / Peter Yun / Cy M Jeffries / David Langley / Roland Gamsjaeger / W Bret Church / Neil Hunter / Charles A Collyer /
Abstract: High-molecular-weight arginine- and lysine-specific (Kgp) gingipains are essential virulence factors expressed by the oral pathogen Porphyromonas gingivalis. Haemagglutinin/adhesin (HA) regions of ...High-molecular-weight arginine- and lysine-specific (Kgp) gingipains are essential virulence factors expressed by the oral pathogen Porphyromonas gingivalis. Haemagglutinin/adhesin (HA) regions of these proteases have been implicated in targeting catalytic domains to biological substrates and in other adhesive functions. We now report the crystal structure of the K3 adhesin domain/module of Kgp, which folds into the distinct β-jelly roll sandwich topology previously observed for K2. A conserved structural feature of K3, previously observed in the Kgp K2 module, is the half-way point anchoring of the surface exposed loops via an arginine residue found in otherwise highly variable sequences. Small-angle X-ray scattering data for the recombinant construct K1K2K3 confirmed a structure comprising a tandem repeat of three homologous modules, K1, K2 and K3 while also indicating an unusual 'y'-shape arrangement of the modules connected by variable linker sequences. Only the K2 and K3 modules and a K1K2 construct were observed to be potently haemolytic. K2, K3 and the K1K2 construct showed preferential recognition of haem-albumin over albumin whereas only low affinity binding was detected for K1 and the K1K2K3 construct. The data indicate replication of some biological functions over the three adhesin domains of Kgp while other functions are restricted.
#1: Journal: Eur J Microbiol Immunol / Year: 2011
Title: Gingipains from Porphyromonas gingivalis complex domain structures confer diverse functions.
Authors: Li, N. / Collyer, C.A.
#2: Journal: Eur J Microbiol Immunol / Year: 2013
Title: The lysine gingipain adhesin domains from porphyromonas gingivalis interact with erythrocytes and albumin: Structures correlate to function.
Authors: Li, N. / Collyer, C.A.
History
DepositionMar 5, 2010Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 23, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 18, 2013Group: Database references
Revision 1.3Nov 8, 2017Group: Refinement description / Category: software
Revision 1.4Nov 1, 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_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_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_asym_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_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_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_ptnr1_label_alt_id / _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
C: Lysine specific cysteine protease
D: Lysine specific cysteine protease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,44221
Polymers75,9144
Non-polymers52817
Water14,862825
1
A: Lysine specific cysteine protease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,1286
Polymers18,9791
Non-polymers1495
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Lysine specific cysteine protease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,1286
Polymers18,9791
Non-polymers1495
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Lysine specific cysteine protease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,1055
Polymers18,9791
Non-polymers1264
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Lysine specific cysteine protease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,0824
Polymers18,9791
Non-polymers1033
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)43.251, 123.131, 62.614
Angle α, β, γ (deg.)90.000, 91.250, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Lysine specific cysteine protease


Mass: 18978.600 Da / Num. of mol.: 4 / Fragment: K3 cleaved adhesin domain, residues 1427-1602
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: Q51817*PLUS
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Ca
#3: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 825 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsSEQUENCE DISCREPANCY, H1448 AND H1479 IN ORIGINAL GENE BANK ENTRY ARE D1448 AND Y1479 RESPECTIVELY.

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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: 2.2 Å3/Da / Density % sol: 43.98 % / Mosaicity: 0.471 °
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.2M Calcium acetate, 30% PEG 8000, 0.1M Na cacodylate, pH 6.5, vapor diffusion, sitting drop, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.95663 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Jan 30, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95663 Å / Relative weight: 1
ReflectionResolution: 1.56→50 Å / Num. obs: 89782 / % possible obs: 96.7 % / Redundancy: 2.4 % / Biso Wilson estimate: 15.1 Å2 / Rmerge(I) obs: 0.032 / Χ2: 1 / Net I/σ(I): 19.1
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.56-1.592.20.16134010.995173.2
1.59-1.622.40.15444351.009196.4
1.62-1.652.40.13544881.008196.5
1.65-1.682.40.11644670.996196.8
1.68-1.722.40.10645030.998196.9
1.72-1.762.40.09744601.001197
1.76-1.82.40.08545411.005197.1
1.8-1.852.40.07344851.007197.6
1.85-1.92.40.0645340.998197.4
1.9-1.972.40.0545680.992197.7
1.97-2.042.40.04445021197.9
2.04-2.122.40.03845400.995198.3
2.12-2.212.40.03745710.996198.2
2.21-2.332.40.03345610.992198.5
2.33-2.482.40.03145771198.6
2.48-2.672.40.02945941.007198.8
2.67-2.942.40.02546190.997199.1
2.94-3.362.40.02246350.995199.3
3.36-4.232.30.02146360.993199.4
4.23-502.30.02446651.009198.7

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACT3.1data extraction
Blu-Icedata collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3KM5

3km5


Resolution: 1.56→23.24 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.954 / WRfactor Rfree: 0.203 / WRfactor Rwork: 0.169 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.896 / SU B: 1.379 / SU ML: 0.05 / SU R Cruickshank DPI: 0.08 / SU Rfree: 0.082 / Cross valid method: THROUGHOUT / ESU R: 0.08 / ESU R Free: 0.082 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.191 4535 5.1 %RANDOM
Rwork0.158 ---
obs0.159 89740 97.29 %-
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: 52.21 Å2 / Biso mean: 18.413 Å2 / Biso min: 6.98 Å2
Baniso -1Baniso -2Baniso -3
1--0.24 Å20 Å2-0.31 Å2
2---1.14 Å20 Å2
3---1.37 Å2
Refinement stepCycle: LAST / Resolution: 1.56→23.24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5240 0 17 825 6082
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0225432
X-RAY DIFFRACTIONr_bond_other_d0.0010.023367
X-RAY DIFFRACTIONr_angle_refined_deg1.5511.9177466
X-RAY DIFFRACTIONr_angle_other_deg0.93438245
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2815703
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.92225.451255
X-RAY DIFFRACTIONr_dihedral_angle_3_deg9.27315706
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.5991510
X-RAY DIFFRACTIONr_chiral_restr0.0920.2821
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0216304
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021114
X-RAY DIFFRACTIONr_mcbond_it1.92323465
X-RAY DIFFRACTIONr_mcbond_other0.65121418
X-RAY DIFFRACTIONr_mcangle_it2.75835567
X-RAY DIFFRACTIONr_scbond_it3.32741967
X-RAY DIFFRACTIONr_scangle_it4.65261892
LS refinement shellResolution: 1.563→1.604 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.241 313 -
Rwork0.183 5756 -
all-6069 -
obs-6069 88.77 %

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