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- PDB-3l94: Structure of PvdQ covalently acylated with myristate -

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Basic information

Entry
Database: PDB / ID: 3l94
TitleStructure of PvdQ covalently acylated with myristate
Components
  • Acyl-homoserine lactone acylase pvdQ subunit alpha
  • Acyl-homoserine lactone acylase pvdQ subunit beta
KeywordsHYDROLASE / PvdQ / pyoverdine / acylase / NTN hydrolase / Quorum sensing / Zymogen
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
MYRISTIC ACID / Acyl-homoserine lactone acylase PvdQ
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.95 Å
AuthorsDrake, E.J. / Gulick, A.M.
CitationJournal: Acs Chem.Biol. / Year: 2011
Title: Structural characterization and high-throughput screening of inhibitors of PvdQ, an NTN hydrolase involved in pyoverdine synthesis.
Authors: Drake, E.J. / Gulick, A.M.
History
DepositionJan 4, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 26, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Apr 17, 2013Group: Database references

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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)80,49022
Polymers79,0832
Non-polymers1,40820
Water5,981332
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12100 Å2
ΔGint11 kcal/mol
Surface area27790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)120.249, 165.501, 94.415
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Acyl-homoserine lactone acylase pvdQ subunit alpha / Acyl-HSL acylase pvdQ subunit alpha


Mass: 18592.918 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Strain: PA01 / 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 beta / Acyl-HSL acylase pvdQ subunit beta


Mass: 60489.918 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Strain: PA01 / Gene: PA2385, pvdQ, qsc112 / Production host: Escherichia coli (E. coli)
References: UniProt: Q9I194, acyl-homoserine-lactone acylase
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 19 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-MYR / MYRISTIC ACID / Myristic acid


Mass: 228.371 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H28O2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 332 / 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: 2.97 Å3/Da / Density % sol: 58.58 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 10-15% PEG4000, 50-100 mM RbCl, 50 mM HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.9795 / Wavelength: 0.97837, 0.97887, 0.9558
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Dec 8, 2008
RadiationMonochromator: Double crystal monochrometer / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97951
20.978371
30.978871
40.95581
ReflectionResolution: 1.95→30 Å / Num. all: 68791 / Num. obs: 68757 / % possible obs: 100 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Biso Wilson estimate: 20.8 Å2 / Rmerge(I) obs: 0.087 / Net I/σ(I): 13.3
Reflection shellResolution: 1.95→2.05 Å / Rmerge(I) obs: 0.497 / Mean I/σ(I) obs: 2.3 / % possible all: 99.7

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Processing

Software
NameVersionClassification
SSRLWebIcedata collection
SOLVEphasing
REFMAC5.5.0088refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MAD / Resolution: 1.95→29.94 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.939 / SU B: 6.039 / SU ML: 0.079 / Cross valid method: THROUGHOUT / ESU R: 0.129 / ESU R Free: 0.119 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS, TLS Refinement used near completion
RfactorNum. reflection% reflectionSelection details
Rfree0.19985 3448 5 %RANDOM
Rwork0.17268 ---
all0.17407 68791 --
obs0.17407 65298 99.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 24.208 Å2
Baniso -1Baniso -2Baniso -3
1--0.38 Å2-0 Å20 Å2
2--0.69 Å20 Å2
3----0.31 Å2
Refinement stepCycle: LAST / Resolution: 1.95→29.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5467 0 91 332 5890
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0225706
X-RAY DIFFRACTIONr_angle_refined_deg1.3431.9637730
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8915713
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.40923.26273
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.13115869
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.2441556
X-RAY DIFFRACTIONr_chiral_restr0.0920.2823
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0214449
X-RAY DIFFRACTIONr_mcbond_it0.6571.53541
X-RAY DIFFRACTIONr_mcangle_it1.20425644
X-RAY DIFFRACTIONr_scbond_it2.18432165
X-RAY DIFFRACTIONr_scangle_it3.6474.52083
LS refinement shellResolution: 1.948→1.998 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.284 246 -
Rwork0.246 4603 -
obs--96.34 %
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)
10.4212-0.1115-0.12970.17650.16720.5026-0.0191-0.002-0.05370.02640.01050.00690.0549-0.04280.00860.0724-0.00380.0070.0950.01040.086626.88338.15956.45
20.2256-0.0348-0.14450.15840.04620.33910.0176-0.03110.00670.01420.0209-0.003-0.1024-0.0378-0.03860.1154-0.00060.00540.08-0.00660.08530.30658.77561.904
30.4065-0.1553-0.1790.1405-0.05240.2933-0.0008-0.0565-0.00820.0111-0.0044-0.0319-0.01990.08960.00520.054-0.014-0.00590.1077-0.01040.090749.01342.48752.444
40.1673-0.06020.00420.5674-0.3880.87570.09320.01390.0213-0.1056-0.003-0.0815-0.25460.0855-0.09020.2402-0.04750.06980.0452-0.01580.102139.98471.3943.503
51.04180.54110.18371.3057-0.79542.73380.03210.1054-0.1224-0.29140.0189-0.2001-0.02040.1872-0.05110.31770.02070.09330.0281-0.0190.066640.87969.90929.845
60.37220.1237-0.33480.463-0.08110.7530.00340.04740.0279-0.06730.02290.0443-0.1564-0.1964-0.02630.10370.0342-0.00580.09170.00290.055220.38360.26150.338
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A29 - 191
2X-RAY DIFFRACTION2B217 - 279
3X-RAY DIFFRACTION3B280 - 476
4X-RAY DIFFRACTION4B477 - 575
5X-RAY DIFFRACTION5B576 - 636
6X-RAY DIFFRACTION6B637 - 762

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