[English] 日本語
Yorodumi
- PDB-4rbm: Porphyromonas gingivalis gingipain K (Kgp) catalytic and immunogl... -

+
Open data


ID or keywords:

Loading...

-
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, 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
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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
Components

-
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

-
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

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbjlvh1.pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more