[English] 日本語
Yorodumi
- PDB-4bth: The LeuA146Trp,PheB24Tyr Double Mutant of the Quorum Quenching N-... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4bth
TitleThe LeuA146Trp,PheB24Tyr Double Mutant of the Quorum Quenching N-acyl Homoserine Lactone Acylase PvdQ Has an Altered Substrate Specificity Towards Small Acyl Chains
Components
  • ACYL-HOMOSERINE LACTONE ACYLASE PVDQ SUBUNIT ALPHA
  • ACYL-HOMOSERINE LACTONE ACYLASE PVDQ SUBUNIT BETA
KeywordsHYDROLASE / ZYMOGEN / QUORUM QUENCHING
Function / homology
Function and homology information


acyl-homoserine-lactone acylase / : / pyoverdine biosynthetic process / hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amides / bacterial-type flagellum-dependent swarming motility / quorum sensing / single-species biofilm formation / antibiotic biosynthetic process / periplasmic space / response to antibiotic ...acyl-homoserine-lactone acylase / : / pyoverdine biosynthetic process / hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amides / bacterial-type flagellum-dependent swarming motility / quorum sensing / single-species biofilm formation / antibiotic biosynthetic process / periplasmic space / response to antibiotic / identical protein binding / cytoplasm
Similarity search - Function
Penicillin amidase (Acylase) alpha subunit, N-terminal domain / Aminohydrolase, alpha-helical knob region / Penicillin Amidohydrolase, domain 1 / Penicillin Amidohydrolase; domain 1 / Penicillin G acylase, beta-roll domain / Aminohydrolase, N-terminal nucleophile (Ntn) domain, beta-sheet knob region / Penicillin/GL-7-ACA/AHL acylase / Penicillin/GL-7-ACA/AHL/aculeacin-A acylase / Penicillin amidase type, domain 1 / Penicillin amidase type, N-terminal domain, B-knob ...Penicillin amidase (Acylase) alpha subunit, N-terminal domain / Aminohydrolase, alpha-helical knob region / Penicillin Amidohydrolase, domain 1 / Penicillin Amidohydrolase; domain 1 / Penicillin G acylase, beta-roll domain / Aminohydrolase, N-terminal nucleophile (Ntn) domain, beta-sheet knob region / Penicillin/GL-7-ACA/AHL acylase / Penicillin/GL-7-ACA/AHL/aculeacin-A acylase / Penicillin amidase type, domain 1 / Penicillin amidase type, N-terminal domain, B-knob / Penicillin amidase type, A-knob / Penicillin amidase / Aminohydrolase, N-terminal nucleophile (Ntn) domain / Glutamine Phosphoribosylpyrophosphate, subunit 1, domain 1 / Nucleophile aminohydrolases, N-terminal / 4-Layer Sandwich / Roll / Orthogonal Bundle / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Acyl-homoserine lactone acylase PvdQ
Similarity search - Component
Biological speciesPSEUDOMONAS AERUGINOSA (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsKoch, G. / Nadal-Jimenez, P. / Reis, C.R. / Muntendam, R. / Bokhove, M. / Melillo, E. / Dijkstra, B.W. / Cool, R.H. / Quax, W.J.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2014
Title: Reducing Virulence of the Human Pathogen Burkholderia by Altering the Substrate Specificity of the Quorum-Quenching Acylase Pvdq
Authors: Koch, G. / Nadal-Jimenez, P. / Reis, C.R. / Muntendam, R. / Bokhove, M. / Melillo, E. / Dijkstra, B.W. / Cool, R.H. / Quax, W.J.
History
DepositionJun 18, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 22, 2014Provider: repository / Type: Initial release
Revision 1.1Feb 5, 2014Group: Database references
Revision 1.2Feb 12, 2014Group: Database references
Revision 1.3Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: ACYL-HOMOSERINE LACTONE ACYLASE PVDQ SUBUNIT ALPHA
B: ACYL-HOMOSERINE LACTONE ACYLASE PVDQ SUBUNIT BETA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,6327
Polymers79,1722
Non-polymers4605
Water4,576254
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9210 Å2
ΔGint-57.3 kcal/mol
Surface area28130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)121.353, 167.133, 94.443
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

-
Components

#1: Protein ACYL-HOMOSERINE LACTONE ACYLASE PVDQ SUBUNIT ALPHA / AHL ACYLASE PVDQ / ACYL-HSL ACYLASE PVDQ / ACYL-HSL ACYLASE PVDQ SUBUNIT ALPHA /


Mass: 18665.969 Da / Num. of mol.: 1 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) PSEUDOMONAS AERUGINOSA (bacteria) / Strain: PAO1 / Description: HOLLOWAY COLLECTION / Plasmid: PMCTNDE / Production host: ESCHERICHIA COLI K-12 (bacteria) / Variant (production host): DH10B
References: UniProt: Q9I194, acyl-homoserine-lactone acylase
#2: Protein ACYL-HOMOSERINE LACTONE ACYLASE PVDQ SUBUNIT BETA / AHL ACYLASE PVDQ / ACYL-HSL ACYLASE PVDQ / ACYL-HSL ACYLASE PVDQ SUBUNIT BETA


Mass: 60505.918 Da / Num. of mol.: 1 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) PSEUDOMONAS AERUGINOSA (bacteria) / Strain: PAO1 / Description: HOLLOWAY COLLECTION / Plasmid: PMCTNDE / Production host: ESCHERICHIA COLI K-12 (bacteria) / Variant (production host): DH10B
References: UniProt: Q9I194, acyl-homoserine-lactone acylase
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


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


Mass: 18.015 Da / Num. of mol.: 254 / 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: 3.03 Å3/Da / Density % sol: 59.4 % / Description: NONE
Crystal growpH: 9.1
Details: PROTEIN WAS CRYSTALLIZED FROM 24% PEG 6000, 100 MM BICINE PH 9.1

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.9786
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 22, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9786 Å / Relative weight: 1
ReflectionResolution: 1.9→83.57 Å / Num. obs: 71419 / % possible obs: 94.6 % / Observed criterion σ(I): 1 / Redundancy: 4.82 % / Biso Wilson estimate: 29.3 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 8.61
Reflection shellResolution: 1.9→2 Å / Redundancy: 4.81 % / Rmerge(I) obs: 0.74 / Mean I/σ(I) obs: 2.21 / % possible all: 96.8

-
Processing

Software
NameVersionClassification
REFMAC5.6.0091refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2WYE

2wye


Resolution: 1.9→62.584 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.955 / SU B: 5.44 / SU ML: 0.081 / Cross valid method: THROUGHOUT / ESU R: 0.128 / ESU R Free: 0.12 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.2074 3591 5.05 %RANDOM
Rwork0.1794 ---
obs0.181 67730 94.198 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL PLUS MASK
Displacement parametersBiso mean: 37.128 Å2
Baniso -1Baniso -2Baniso -3
1--0.599 Å20 Å20 Å2
2--1.175 Å20 Å2
3----0.576 Å2
Refinement stepCycle: LAST / Resolution: 1.9→62.584 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5537 0 30 254 5821
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0225715
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.1751.9587769
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.615712
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.27823.357280
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.07115896
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.3571557
X-RAY DIFFRACTIONr_chiral_restr0.0810.2828
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0214487
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1990.22706
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.30.23821
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1140.2195
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_it0.0110.15715
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.0180.157769
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it0.0330.21945
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it0.0170.47305
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.327 231 -
Rwork0.285 4904 -
obs--96.486 %
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)
11.38691.1251-1.91572.5848-1.63713.87030.00050.34160.0509-0.52080.1265-0.2148-0.2018-0.1862-0.12710.35660.03980.05180.17380.0080.144332.740768.750231.199
22.9364-0.1652-0.68950.454-0.1021.1922-0.06560.0593-0.1468-0.06460.0147-0.07220.0710.09450.05090.03440.00650.00750.03050.00140.034145.05535.309147.1397
31.22620.134-0.12280.9139-0.0231.13530.0013-0.10810.15830.06890.0349-0.0233-0.2524-0.0364-0.03630.0620.01660.00180.0335-0.01480.022630.073557.029661.0042
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1B323 - 480
2X-RAY DIFFRACTION2A51 - 95
3X-RAY DIFFRACTION2A129 - 168
4X-RAY DIFFRACTION2B75 - 155
5X-RAY DIFFRACTION2B206 - 250
6X-RAY DIFFRACTION3A6 - 50
7X-RAY DIFFRACTION3A96 - 128
8X-RAY DIFFRACTION3B1 - 74
9X-RAY DIFFRACTION3B156 - 205
10X-RAY DIFFRACTION3B251 - 322
11X-RAY DIFFRACTION3B481 - 546

+
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