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- PDB-4m1j: Crystal structure of Pseudomonas aeruginosa PvdQ in complex with ... -

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Basic information

Entry
Database: PDB / ID: 4m1j
TitleCrystal structure of Pseudomonas aeruginosa PvdQ in complex with a transition state analogue
Components
  • Acyl-homoserine lactone acylase PvdQ subunit alpha
  • Acyl-homoserine lactone acylase PvdQ subunit beta
KeywordsHYDROLASE / transition state analogue / heterodimer / acylase / boronic acid / secreted
Function / homology
Function and homology information


acyl-homoserine-lactone acylase / short-chain fatty acyl-CoA dehydrogenase activity / pyoverdine biosynthetic process / hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amides / quorum sensing / bacterial-type flagellum-dependent swarming motility / single-species biofilm formation / antibiotic biosynthetic process / periplasmic space / response to antibiotic ...acyl-homoserine-lactone acylase / short-chain fatty acyl-CoA dehydrogenase activity / pyoverdine biosynthetic process / hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amides / quorum sensing / bacterial-type flagellum-dependent swarming motility / 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
tridecylboronic acid / Acyl-homoserine lactone acylase PvdQ
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.8 Å
AuthorsWu, R. / Clevenger, K. / Er, J. / Fast, W.L. / Liu, D.
CitationJournal: Acs Chem.Biol. / Year: 2013
Title: Rational Design of a Transition State Analogue with Picomolar Affinity for Pseudomonas aeruginosa PvdQ, a Siderophore Biosynthetic Enzyme.
Authors: Clevenger, K.D. / Wu, R. / Er, J.A. / Liu, D. / Fast, W.
History
DepositionAug 2, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 28, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 6, 2013Group: Database references
Revision 1.2Nov 15, 2017Group: Refinement description / Category: software / Item: _software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
C: Acyl-homoserine lactone acylase PvdQ subunit beta
A: Acyl-homoserine lactone acylase PvdQ subunit alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,69523
Polymers78,6252
Non-polymers2,07021
Water10,773598
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12900 Å2
ΔGint-61 kcal/mol
Surface area27440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)120.948, 166.433, 94.208
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Acyl-homoserine lactone acylase PvdQ subunit beta / Acyl-HSL acylase PvdQ subunit beta / PvdQ NTN-hydrolase Acylase beta subunit


Mass: 60632.078 Da / Num. of mol.: 1 / Fragment: UNP residues 217-762
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Gene: PA2385, pvdQ, qsc112 / Production host: Escherichia coli (E. coli)
References: UniProt: Q9I194, acyl-homoserine-lactone acylase
#2: Protein Acyl-homoserine lactone acylase PvdQ subunit alpha / Acyl-HSL acylase PvdQ subunit alpha / PvdQ NTN-hydrolase Acylase alpha subunit


Mass: 17993.191 Da / Num. of mol.: 1 / Fragment: UNP residues 28-192
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Gene: pvdQ, qsc112, PA2385 / Production host: Escherichia coli (E. coli)
References: UniProt: Q9I194, acyl-homoserine-lactone acylase
#3: Chemical ChemComp-B0S / tridecylboronic acid


Mass: 228.179 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C13H29BO2
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 20 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 598 / Source method: isolated from a natural source / Formula: H2O

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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: 3.01 Å3/Da / Density % sol: 59.2 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.05 M HEPES, 80 mM rubidium chloride, 9% PEG4000, 20% glycerol, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.0332 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Aug 22, 2012 / Details: mirrors
RadiationMonochromator: Double crystal cryo-cooled Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 1.699→97.841 Å / Num. all: 104451 / Num. obs: 103032 / % possible obs: 99.7 % / Observed criterion σ(I): 2 / Redundancy: 6.3 % / Biso Wilson estimate: 23.68 Å2 / Rmerge(I) obs: 0.124
Reflection shellHighest resolution: 1.699 Å

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
PHASERphasing
PHENIX1.8_1069refinement
PDB_EXTRACT3.11data extraction
HKL-2000data collection
DENZOdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→41 Å / Occupancy max: 1 / Occupancy min: 0.4 / FOM work R set: 0.8749 / SU ML: 0.18 / σ(F): 2.1 / Phase error: 19.59 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1878 5146 5 %RODOM
Rwork0.1623 ---
obs0.1636 103012 98.72 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 97.32 Å2 / Biso mean: 29.4603 Å2 / Biso min: 11.41 Å2
Refinement stepCycle: LAST / Resolution: 1.8→41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5521 0 136 598 6255
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0125825
X-RAY DIFFRACTIONf_angle_d1.2867888
X-RAY DIFFRACTIONf_chiral_restr0.108832
X-RAY DIFFRACTIONf_plane_restr0.0051042
X-RAY DIFFRACTIONf_dihedral_angle_d14.7532173
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.6995-1.71880.31691590.28992965312491
1.7188-1.7390.27861680.27673218338698
1.739-1.76020.28231660.27033226339299
1.7602-1.78250.30571870.26293223341098
1.7825-1.8060.27451480.25193240338899
1.806-1.83070.28261600.23593225338599
1.8307-1.85690.23881780.22313228340699
1.8569-1.88460.24411680.20793263343199
1.8846-1.9140.23391660.19723235340199
1.914-1.94540.23561570.19833255341299
1.9454-1.9790.21641770.19433239341699
1.979-2.0150.23831760.2053145332196
2.015-2.05370.27111730.22333064323793
2.0537-2.09560.20241900.16833232342299
2.0956-2.14120.17961850.16073274345999
2.1412-2.1910.16621670.15583270343799
2.191-2.24580.19421780.14793253343199
2.2458-2.30650.19851670.148632623429100
2.3065-2.37440.17351720.14913293346599
2.3744-2.4510.21421810.155132913472100
2.451-2.53860.19452020.156432433445100
2.5386-2.64030.19141500.155233373487100
2.6403-2.76040.17311810.155132723453100
2.7604-2.90590.18021710.153933333504100
2.9059-3.0880.18941600.14933163476100
3.088-3.32630.16681680.144433463514100
3.3263-3.6610.1531600.143233593519100
3.661-4.19050.1441730.133633513524100
4.1905-5.27860.14971780.13733953573100
5.2786-48.94090.20241800.174335133693100
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)
10.7991-0.31540.3480.4498-0.08380.740.04-0.0875-0.0947-0.00060.02480.09770.1262-0.1541-0.06470.1309-0.03910.00070.15090.00650.13715.802132.92337.1449
21.09750.51130.89631.37150.71412.14310.04210.1818-0.124-0.25690.05770.0560.29140.202-0.10680.28330.0588-0.02340.1596-0.01720.191132.444217.3218-6.0082
30.37110.23940.0440.16310.01260.03560.10950.1288-0.2058-0.36460.3842-0.0147-0.12460.3379-0.35610.42850.0535-0.05210.2531-0.02920.276841.713245.479831.0939
44.9092-3.7405-3.74064.76113.28086.5886-0.1069-0.27630.07680.28980.2309-0.14740.4010.4704-0.05510.14490.0203-0.02440.1818-0.01680.130343.952530.123221.2276
51.4829-0.80271.45351.3931-1.26232.4439-0.04150.08680.0988-0.0624-0.0447-0.1003-0.05510.13750.0950.1323-0.03150.00580.1496-0.01010.156934.613345.81524.2624
63.28550.01830.40856.5076-5.24424.5026-0.1018-0.30590.2170.4650.12990.2838-0.9286-0.3735-0.07690.20140.02-0.01110.2058-0.06610.221822.135951.521115.2146
75.07770.0288-2.73421.37530.44623.6076-0.0177-0.3040.33210.10660.1043-0.1296-0.0580.283-0.1250.13560.0011-0.03450.1558-0.01310.155742.037344.498515.8601
82.2122.1834-3.46282.3655-2.64389.62590.17480.06280.53750.02250.04370.0205-0.39940.1516-0.15750.1644-0.0461-0.03470.20260.00290.223642.448950.89155.7971
92.6545-0.36452.01391.0371-0.14613.2820.05740.1305-0.007-0.0047-0.0150.0667-0.00690.0123-0.05270.13830.00950.02930.1680.00310.165620.869446.37820.3875
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'C' and (resid 218 through 528 )C0
2X-RAY DIFFRACTION2chain 'C' and (resid 529 through 764 )C0
3X-RAY DIFFRACTION3chain 'A' and (resid 28 through 33 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 34 through 49 )A0
5X-RAY DIFFRACTION5chain 'A' and (resid 50 through 106 )A0
6X-RAY DIFFRACTION6chain 'A' and (resid 107 through 120 )A0
7X-RAY DIFFRACTION7chain 'A' and (resid 121 through 150 )A0
8X-RAY DIFFRACTION8chain 'A' and (resid 151 through 158 )A0
9X-RAY DIFFRACTION9chain 'A' and (resid 159 through 192 )A0

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