[English] 日本語
Yorodumi
- PDB-6n9r: Structure of the Quorum Quenching lactonase from Parageobacillus ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6n9r
TitleStructure of the Quorum Quenching lactonase from Parageobacillus caldoxylosilyticus bound to substrate 3-oxo-C12-AHL
ComponentsPutative hydrolase
KeywordsHYDROLASE / lactonase / quorum sensing / thermophile / MLL / quorum quenching / AHL
Function / homology
Function and homology information


hydrolase activity / metal ion binding
Similarity search - Function
: / Metallo-beta-lactamase superfamily / Metallo-beta-lactamase superfamily / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like / Metallo-beta-lactamase; Chain A / Metallo-beta-lactamase / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like / 4-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / : / : / N-3-OXO-DODECANOYL-L-HOMOSERINE LACTONE / TRIETHYLENE GLYCOL / Putative hydrolase
Similarity search - Component
Biological speciesParageobacillus caldoxylosilyticus NBRC 107762 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsBergonzi, C. / Schwab, M. / Elias, M.
CitationJournal: Chembiochem / Year: 2019
Title: The Structural Determinants Accounting for the Broad Substrate Specificity of the Quorum Quenching Lactonase GcL.
Authors: Bergonzi, C. / Schwab, M. / Naik, T. / Elias, M.
History
DepositionDec 3, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 3, 2019Provider: repository / Type: Initial release
Revision 1.1Aug 14, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Oct 11, 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 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Putative hydrolase
P: Putative hydrolase
X: Putative hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)107,26145
Polymers103,1373
Non-polymers4,12442
Water8,125451
1
P: Putative hydrolase
X: Putative hydrolase
hetero molecules

P: Putative hydrolase
X: Putative hydrolase
hetero molecules

A: Putative hydrolase
hetero molecules

A: Putative hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)214,52290
Polymers206,2736
Non-polymers8,24984
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_554-x,y,-z-11
crystal symmetry operation3_454x-1/2,y+1/2,z-11
crystal symmetry operation4_555-x+1/2,y+1/2,-z1
Buried area34590 Å2
ΔGint-338 kcal/mol
Surface area62020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)145.010, 108.590, 78.600
Angle α, β, γ (deg.)90.00, 115.75, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11P-433-

HOH

-
Components

-
Protein , 1 types, 3 molecules APX

#1: Protein Putative hydrolase


Mass: 34378.914 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Parageobacillus caldoxylosilyticus NBRC 107762 (bacteria)
Gene: GCA01S_030_00190 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A023DFE8

-
Non-polymers , 9 types, 493 molecules

#2: Chemical ChemComp-CO / COBALT (II) ION


Mass: 58.933 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Co
#3: Chemical ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Fe
#4: Chemical ChemComp-OHN / N-3-OXO-DODECANOYL-L-HOMOSERINE LACTONE


Mass: 297.390 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C16H27NO4
#5: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H3O2
#6: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 17 / Source method: obtained synthetically / Formula: C2H6O2
#7: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#8: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#9: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: SO4
#10: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 451 / 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: 2.86 Å3/Da / Density % sol: 57.03 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop
Details: Concentrated protein samples 10mg.mL-1, ammonium sulfate 1 to 2.25M, 0.1M sodium acetate. Soaking in 20 mM of C12 AHL for 5 min. Diffraction quality crystals appeared after 1 d at 292 K
PH range: 4.0 to 5.5

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.03333 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 1, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03333 Å / Relative weight: 1
ReflectionResolution: 1.75→70.8 Å / Num. obs: 109519 / % possible obs: 99.2 % / Redundancy: 3.98 % / CC1/2: 0.999 / Rrim(I) all: 0.059 / Rsym value: 0.051 / Net I/σ(I): 15.21
Reflection shellResolution: 1.75→1.85 Å / Redundancy: 4.07 % / Mean I/σ(I) obs: 3.32 / Num. unique obs: 16825 / CC1/2: 0.947 / Rrim(I) all: 0.48 / Rsym value: 0.419 / % possible all: 99.5

-
Processing

Software
NameVersionClassification
REFMAC5.8.0222refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6N9I

6n9i


Resolution: 1.75→70.8 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.931 / SU B: 6.959 / SU ML: 0.097 / Cross valid method: THROUGHOUT / ESU R: 0.153 / ESU R Free: 0.115 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23481 5476 5 %RANDOM
Rwork0.17597 ---
obs0.17894 104043 99.33 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 23.912 Å2
Baniso -1Baniso -2Baniso -3
1-0.1 Å20 Å2-0.05 Å2
2---0.04 Å2-0 Å2
3----0.01 Å2
Refinement stepCycle: 1 / Resolution: 1.75→70.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6711 0 250 451 7412
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0020.0147611
X-RAY DIFFRACTIONr_bond_other_d00.0186630
X-RAY DIFFRACTIONr_angle_refined_deg0.5951.68110302
X-RAY DIFFRACTIONr_angle_other_deg0.9871.69115623
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.655918
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.53823.093430
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.905151262
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.3881542
X-RAY DIFFRACTIONr_chiral_restr0.030.2941
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.028637
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021437
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.3761.9743572
X-RAY DIFFRACTIONr_mcbond_other3.321.9723568
X-RAY DIFFRACTIONr_mcangle_it3.8862.9764520
X-RAY DIFFRACTIONr_mcangle_other3.8882.9774521
X-RAY DIFFRACTIONr_scbond_it5.0442.5294039
X-RAY DIFFRACTIONr_scbond_other5.0422.5294039
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.8363.5975783
X-RAY DIFFRACTIONr_long_range_B_refined5.25724.4268650
X-RAY DIFFRACTIONr_long_range_B_other5.25324.4258650
X-RAY DIFFRACTIONr_rigid_bond_restr10.352314240
X-RAY DIFFRACTIONr_sphericity_free26.5585250
X-RAY DIFFRACTIONr_sphericity_bonded15.976514248
LS refinement shellResolution: 1.75→1.795 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.304 403 -
Rwork0.228 7660 -
obs--99.42 %

+
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://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