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- PDB-5dwz: Structural and functional characterization of PqsBC, a condensing... -

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Basic information

Entry
Database: PDB / ID: 5dwz
TitleStructural and functional characterization of PqsBC, a condensing enzyme in the biosynthesis of the Pseudomonas aeruginosa quinolone signal
Components
  • 3-oxoacyl-(Acyl carrier protein) synthase III
  • 3-oxoacyl-[acyl-carrier-protein] synthase 3
KeywordsTRANSFERASE / PROTEIN COMPLEX / PqsB / PqsC
Function / homology
Function and homology information


2-heptyl-4(1H)-quinolone synthase / beta-ketoacyl-[acyl-carrier-protein] synthase III / beta-ketoacyl-acyl-carrier-protein synthase III activity / secondary metabolite biosynthetic process / acyltransferase activity / 3-oxoacyl-[acyl-carrier-protein] synthase activity / fatty acid biosynthetic process / cytoplasm
Similarity search - Function
3-Oxoacyl-[acyl-carrier-protein (ACP)] synthase III / 3-Oxoacyl-[acyl-carrier-protein (ACP)] synthase III / 3-Oxoacyl-[acyl-carrier-protein (ACP)] synthase III, C-terminal / 3-Oxoacyl-[acyl-carrier-protein (ACP)] synthase III C terminal / Thiolase/Chalcone synthase / Peroxisomal Thiolase; Chain A, domain 1 / Thiolase-like / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / PHOSPHATE ION / 3-oxoacyl-(Acyl carrier protein) synthase III / 3-oxoacyl-ACP synthase III family protein / 2-heptyl-4(1H)-quinolone synthase subunit PqsC / 2-heptyl-4(1H)-quinolone synthase subunit PqsB
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 2.04 Å
AuthorsDrees, S.L. / Li, C. / Prasetya, F. / Saleem, M. / Dreveny, I. / Hennecke, U. / Williams, P. / Emsley, J. / Fetzner, S.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research FoundationFE 383/23-1 Germany
CitationJournal: J.Biol.Chem. / Year: 2016
Title: PqsBC, a Condensing Enzyme in the Biosynthesis of the Pseudomonas aeruginosa Quinolone Signal: CRYSTAL STRUCTURE, INHIBITION, AND REACTION MECHANISM.
Authors: Drees, S.L. / Li, C. / Prasetya, F. / Saleem, M. / Dreveny, I. / Williams, P. / Hennecke, U. / Emsley, J. / Fetzner, S.
History
DepositionSep 23, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Feb 3, 2016Provider: repository / Type: Initial release
Revision 1.1Feb 10, 2016Group: Database references
Revision 1.2Apr 6, 2016Group: Database references
Revision 1.3May 11, 2016Group: Source and taxonomy
Revision 1.4Sep 6, 2017Group: Advisory / Author supporting evidence / Category: pdbx_audit_support / pdbx_unobs_or_zero_occ_atoms / Item: _pdbx_audit_support.funding_organization
Revision 1.5May 8, 2024Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms / struct_conn
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_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
C: 3-oxoacyl-[acyl-carrier-protein] synthase 3
B: 3-oxoacyl-(Acyl carrier protein) synthase III
D: 3-oxoacyl-[acyl-carrier-protein] synthase 3
A: 3-oxoacyl-(Acyl carrier protein) synthase III
F: 3-oxoacyl-[acyl-carrier-protein] synthase 3
E: 3-oxoacyl-(Acyl carrier protein) synthase III
H: 3-oxoacyl-[acyl-carrier-protein] synthase 3
G: 3-oxoacyl-(Acyl carrier protein) synthase III
hetero molecules


Theoretical massNumber of molelcules
Total (without water)279,50347
Polymers275,4378
Non-polymers4,06639
Water19,7261095
1
C: 3-oxoacyl-[acyl-carrier-protein] synthase 3
B: 3-oxoacyl-(Acyl carrier protein) synthase III
F: 3-oxoacyl-[acyl-carrier-protein] synthase 3
E: 3-oxoacyl-(Acyl carrier protein) synthase III
hetero molecules


Theoretical massNumber of molelcules
Total (without water)139,97026
Polymers137,7194
Non-polymers2,25222
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area17010 Å2
ΔGint-151 kcal/mol
Surface area42130 Å2
MethodPISA
2
D: 3-oxoacyl-[acyl-carrier-protein] synthase 3
A: 3-oxoacyl-(Acyl carrier protein) synthase III
H: 3-oxoacyl-[acyl-carrier-protein] synthase 3
G: 3-oxoacyl-(Acyl carrier protein) synthase III
hetero molecules


Theoretical massNumber of molelcules
Total (without water)139,53321
Polymers137,7194
Non-polymers1,81417
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15820 Å2
ΔGint-136 kcal/mol
Surface area42940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.486, 114.960, 289.675
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11C
21D
12C
22F
13C
23H
14B
24A
15B
25E
16B
26G
17D
27F
18D
28H
19A
29E
110A
210G
111F
211H
112E
212G

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1010C3 - 350
2010D3 - 350
1020C3 - 350
2020F3 - 350
1030C3 - 350
2030H3 - 350
1040B1 - 278
2040A1 - 278
1050B1 - 277
2050E1 - 277
1060B1 - 278
2060G1 - 278
1070D3 - 350
2070F3 - 350
1080D3 - 350
2080H3 - 350
1090A1 - 277
2090E1 - 277
10100A1 - 278
20100G1 - 278
10110F3 - 350
20110H3 - 350
10120E1 - 279
20120G1 - 279

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9
10
11
12

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Components

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Protein , 2 types, 8 molecules CDFHBAEG

#1: Protein
3-oxoacyl-[acyl-carrier-protein] synthase 3 / Beta-keto-ACP synthase / Beta-keto-acyl-acyl-carrier-like protein synthase / PQS biosynthesis ...Beta-keto-ACP synthase / Beta-keto-acyl-acyl-carrier-like protein synthase / PQS biosynthesis protein PqsC / Uncharacterized protein


Mass: 38327.531 Da / Num. of mol.: 4 / Mutation: C129A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Gene: pqsC / Plasmid: pET28b / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta2 pLysS
References: UniProt: A0A0C6EZ24, UniProt: Q9I4X1*PLUS, beta-ketoacyl-[acyl-carrier-protein] synthase III
#2: Protein
3-oxoacyl-(Acyl carrier protein) synthase III / Beta-keto-ACP synthase / Beta-keto-acyl-acyl-carrier-like protein synthase / PQS biosynthesis ...Beta-keto-ACP synthase / Beta-keto-acyl-acyl-carrier-like protein synthase / PQS biosynthesis protein PqsB / PqsB


Mass: 30531.760 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Gene: pqsB / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta2 pLysS / References: UniProt: A0A072ZZD2, UniProt: Q9I4X2*PLUS

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Non-polymers , 9 types, 1134 molecules

#3: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 20 / Source method: obtained synthetically / Formula: PO4
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical
ChemComp-MPO / 3[N-MORPHOLINO]PROPANE SULFONIC ACID


Mass: 209.263 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C7H15NO4S / Comment: pH buffer*YM
#6: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#7: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#8: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#9: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H10O3
#10: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#11: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1095 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.41 Å3/Da / Density % sol: 49.01 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: 0.2 M NaCl, 0.1 M Tris pH 8.5, 255 PEG 3350

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.97949 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Oct 19, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 2.04→29.6 Å / Num. obs: 166566 / % possible obs: 99.2 % / Redundancy: 4.5 % / Rmerge(I) obs: 0.069 / Net I/σ(I): 12.5
Reflection shellResolution: 2.04→2.09 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.696 / Mean I/σ(I) obs: 1.9 / % possible all: 96.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0107refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: SIRAS / Resolution: 2.04→144.84 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.939 / SU B: 5.531 / SU ML: 0.147 / Cross valid method: THROUGHOUT / ESU R: 0.202 / ESU R Free: 0.176 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23699 8364 5 %RANDOM
Rwork0.18958 ---
obs0.19196 158109 99.08 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 38.071 Å2
Baniso -1Baniso -2Baniso -3
1-0.68 Å20 Å20 Å2
2---0.29 Å20 Å2
3----0.39 Å2
Refinement stepCycle: LAST / Resolution: 2.04→144.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms18956 0 236 1095 20287
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.01919512
X-RAY DIFFRACTIONr_bond_other_d0.010.0218705
X-RAY DIFFRACTIONr_angle_refined_deg1.8141.98626459
X-RAY DIFFRACTIONr_angle_other_deg2.069342921
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.33552468
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.03123.4844
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.542153125
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.03415173
X-RAY DIFFRACTIONr_chiral_restr0.1080.22949
X-RAY DIFFRACTIONr_gen_planes_refined0.010.02122009
X-RAY DIFFRACTIONr_gen_planes_other0.0070.024351
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_it3.0773.5589891
X-RAY DIFFRACTIONr_mcbond_other3.0773.5589889
X-RAY DIFFRACTIONr_mcangle_it4.1275.31912337
X-RAY DIFFRACTIONr_mcangle_other4.1275.31912338
X-RAY DIFFRACTIONr_scbond_it3.8814.0239621
X-RAY DIFFRACTIONr_scbond_other3.8814.0239621
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.6025.87314118
X-RAY DIFFRACTIONr_long_range_B_refined7.4829.38221682
X-RAY DIFFRACTIONr_long_range_B_other7.4829.38221682
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11C392800.11
12D392800.11
21C390820.12
22F390820.12
31C386160.13
32H386160.13
41B338300.1
42A338300.1
51B329460.12
52E329460.12
61B328400.13
62G328400.13
71D389640.12
72F389640.12
81D385360.13
82H385360.13
91A332020.12
92E332020.12
101A333340.12
102G333340.12
111F388040.13
112H388040.13
121E332560.11
122G332560.11
LS refinement shellResolution: 2.037→2.09 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.321 541 -
Rwork0.291 11338 -
obs--96.58 %

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