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- PDB-5oe6: Crystal structure of the N-terminal domain of PqsA in complex wit... -

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Basic information

Entry
Database: PDB / ID: 5oe6
TitleCrystal structure of the N-terminal domain of PqsA in complex with 6-fluoroanthraniloyl-AMP (crystal form 1)
ComponentsAnthranilate--CoA ligase
KeywordsLIGASE / PQS / PqsA / Anthranilate / Anthraniloyl-AMP / Anthraniloyl-CoA / Pseudomonas Quinolone Signal / Pseudomonas aeruginosa / Quorum Sensing / Aryl-CoA ligase / ANL superfamily / Fluor / 6FABA / 6-fluoroanthranilate / 6-fluoroanthraniloyl-AMP / 6FABA-AMP
Function / homology
Function and homology information


anthranilate-CoA ligase / acid-thiol ligase activity / anthranilate-CoA ligase activity / secondary metabolite biosynthetic process / ATP binding
Similarity search - Function
ANL, N-terminal domain / AMP-binding enzyme, C-terminal domain / AMP-binding enzyme C-terminal domain / AMP-binding, conserved site / Putative AMP-binding domain signature. / AMP-dependent synthetase/ligase / AMP-binding enzyme, C-terminal domain superfamily / AMP-binding enzyme
Similarity search - Domain/homology
6-fluoroanthraniloyl-AMP / TRIETHYLENE GLYCOL / Anthranilate--CoA ligase
Similarity search - Component
Biological speciesPseudomonas aeruginosa PAO1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.67 Å
AuthorsWitzgall, F. / Ewert, W. / Blankenfeldt, W.
CitationJournal: Chembiochem / Year: 2017
Title: Structures of the N-Terminal Domain of PqsA in Complex with Anthraniloyl- and 6-Fluoroanthraniloyl-AMP: Substrate Activation in Pseudomonas Quinolone Signal (PQS) Biosynthesis.
Authors: Witzgall, F. / Ewert, W. / Blankenfeldt, W.
History
DepositionJul 7, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 6, 2017Provider: repository / Type: Initial release
Revision 1.1Oct 25, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Anthranilate--CoA ligase
B: Anthranilate--CoA ligase
C: Anthranilate--CoA ligase
D: Anthranilate--CoA ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)179,6689
Polymers177,5814
Non-polymers2,0885
Water26,0141444
1
A: Anthranilate--CoA ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,8802
Polymers44,3951
Non-polymers4841
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Anthranilate--CoA ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,8802
Polymers44,3951
Non-polymers4841
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Anthranilate--CoA ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,0303
Polymers44,3951
Non-polymers6352
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Anthranilate--CoA ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,8802
Polymers44,3951
Non-polymers4841
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)71.558, 84.130, 138.212
Angle α, β, γ (deg.)90.000, 92.590, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 3 through 12 or (resid 13...
21(chain B and (resid 3 through 12 or (resid 13...
31(chain C and (resid 3 through 12 or (resid 13...
41(chain D and (resid 3 through 18 or resid 20...

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain A and (resid 3 through 12 or (resid 13...A3 - 12
121(chain A and (resid 3 through 12 or (resid 13...A13
131(chain A and (resid 3 through 12 or (resid 13...A3 - 399
141(chain A and (resid 3 through 12 or (resid 13...A3 - 399
151(chain A and (resid 3 through 12 or (resid 13...A3 - 399
161(chain A and (resid 3 through 12 or (resid 13...A3 - 399
171(chain A and (resid 3 through 12 or (resid 13...A3 - 399
181(chain A and (resid 3 through 12 or (resid 13...A3 - 399
211(chain B and (resid 3 through 12 or (resid 13...B3 - 12
221(chain B and (resid 3 through 12 or (resid 13...B13
231(chain B and (resid 3 through 12 or (resid 13...B2 - 900
241(chain B and (resid 3 through 12 or (resid 13...B2 - 900
251(chain B and (resid 3 through 12 or (resid 13...B2 - 900
261(chain B and (resid 3 through 12 or (resid 13...B2 - 900
271(chain B and (resid 3 through 12 or (resid 13...B2 - 900
281(chain B and (resid 3 through 12 or (resid 13...B2 - 900
311(chain C and (resid 3 through 12 or (resid 13...C3 - 12
321(chain C and (resid 3 through 12 or (resid 13...C13
331(chain C and (resid 3 through 12 or (resid 13...C2 - 901
341(chain C and (resid 3 through 12 or (resid 13...C2 - 901
351(chain C and (resid 3 through 12 or (resid 13...C2 - 901
361(chain C and (resid 3 through 12 or (resid 13...C2 - 901
371(chain C and (resid 3 through 12 or (resid 13...C2 - 901
381(chain C and (resid 3 through 12 or (resid 13...C2 - 901
411(chain D and (resid 3 through 18 or resid 20...D3 - 18
421(chain D and (resid 3 through 18 or resid 20...D20 - 30
431(chain D and (resid 3 through 18 or resid 20...D32 - 35
441(chain D and (resid 3 through 18 or resid 20...D37 - 55
451(chain D and (resid 3 through 18 or resid 20...D57 - 67
461(chain D and (resid 3 through 18 or resid 20...D69 - 87
471(chain D and (resid 3 through 18 or resid 20...D88
481(chain D and (resid 3 through 18 or resid 20...D3 - 900
491(chain D and (resid 3 through 18 or resid 20...D3 - 900
4101(chain D and (resid 3 through 18 or resid 20...D3 - 900
4111(chain D and (resid 3 through 18 or resid 20...D3 - 900
4121(chain D and (resid 3 through 18 or resid 20...D3 - 900
4131(chain D and (resid 3 through 18 or resid 20...D3 - 900
4141(chain D and (resid 3 through 18 or resid 20...D3 - 900

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Components

#1: Protein
Anthranilate--CoA ligase


Mass: 44395.195 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa PAO1 (bacteria) / Gene: pqsA, PA0996 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9I4X3, anthranilate-CoA ligase
#2: Chemical
ChemComp-9SN / 6-fluoroanthraniloyl-AMP


Mass: 484.332 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C17H18FN6O8P
#3: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL / Polyethylene glycol


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1444 / 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: 2.34 Å3/Da / Density % sol: 47.44 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.2
Details: 100 tri-sodium citrate, 250 mM ammonium acetate, 27.9% PEG3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 18, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 1.67→46.023 Å / Num. obs: 188926 / % possible obs: 99.6 % / Redundancy: 5.4 % / Biso Wilson estimate: 9.61 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.154 / Rpim(I) all: 0.072 / Rrim(I) all: 0.171 / Net I/σ(I): 8.4
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsCC1/2Rpim(I) allRrim(I) all% possible all
1.67-1.750.8790.6340.4270.98198.9
9.15-46.025.40.060.9970.0280.06698

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Processing

Software
NameVersionClassification
Aimless0.5.23data scaling
PHENIX1.12rc2_2821refinement
PDB_EXTRACT3.22data extraction
XDSdata reduction
Coot0.8.8model building
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.67→46.023 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 1.97 / Phase error: 33.35
RfactorNum. reflection% reflection
Rfree0.3132 9229 4.89 %
Rwork0.2695 --
obs0.2716 188879 99.6 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 72.68 Å2 / Biso mean: 22.2109 Å2 / Biso min: 0.81 Å2
Refinement stepCycle: final / Resolution: 1.67→46.023 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12019 0 228 1444 13691
Biso mean--15.67 22.2 -
Num. residues----1570
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00512609
X-RAY DIFFRACTIONf_angle_d0.77317201
X-RAY DIFFRACTIONf_chiral_restr0.0461865
X-RAY DIFFRACTIONf_plane_restr0.0052362
X-RAY DIFFRACTIONf_dihedral_angle_d16.2117568
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A8551X-RAY DIFFRACTION8.683TORSIONAL
12B8551X-RAY DIFFRACTION8.683TORSIONAL
13C8551X-RAY DIFFRACTION8.683TORSIONAL
14D8551X-RAY DIFFRACTION8.683TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.67-1.6890.35992840.31435913619799
1.689-1.70880.36053110.31745935624699
1.7088-1.72970.34233310.31055836616799
1.7297-1.75160.37462950.30786001629699
1.7516-1.77460.38572880.3075902619099
1.7746-1.79890.35453300.30195951628199
1.7989-1.82460.35582940.29815896619099
1.8246-1.85190.34822930.29325901619499
1.8519-1.88080.33252780.28556032631099
1.8808-1.91170.31223380.283659556293100
1.9117-1.94460.34543180.290459826300100
1.9446-1.980.36023150.286359656280100
1.98-2.01810.34343290.283159636292100
2.0181-2.05930.31452890.271360196308100
2.0593-2.1040.30923180.265360196337100
2.104-2.1530.30253190.262159746293100
2.153-2.20680.31432910.261560026293100
2.2068-2.26650.28952910.266360166307100
2.2665-2.33320.31583100.261559856295100
2.3332-2.40850.30373000.257960106310100
2.4085-2.49460.30073180.251559946312100
2.4946-2.59440.28243010.255460116312100
2.5944-2.71250.31043050.257560546359100
2.7125-2.85550.30723380.250859576295100
2.8555-3.03440.30142820.257560466328100
3.0344-3.26860.30022920.269260596351100
3.2686-3.59740.32243300.265560196349100
3.5974-4.11770.27253050.255760216326100
4.1177-5.18670.27782900.235461026392100
5.1867-46.0410.30133460.28536130647699
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)
10.84720.2983-0.26321.3871-0.11330.57320.01640.00450.03520.0726-0.02160.0975-0.0739-0.0901-0.00670.30230.0193-0.02110.2579-0.04450.116713.95285.71917.542
20.158-0.01820.03620.45960.04410.19070.01480.02740.0757-0.09290.0770.0344-0.139-0.1083-0.07390.41660.01750.01910.27050.01780.176416.4153-4.41535.7868
30.5013-0.2579-0.20430.94110.67450.60230.01110.0261-0.0029-0.0446-0.0193-0.06260.00040.04330.01640.4433-0.0544-0.01480.29430.03640.190116.5224-4.2616-4.5765
40.4329-0.03470.31360.5086-0.2362.313-0.04020.02090.0687-0.00160.02220.0594-0.1027-0.13110.01960.2312-0.0138-0.03170.20380.01290.16734.7833-5.100310.9303
50.13120.14670.35141.31530.52820.98710.072-0.028-0.001-0.0010.003-0.03850.01060.0695-0.05280.27680.0211-0.01490.195-0.00380.095125.7363-8.331217.3305
60.3304-0.0485-0.07410.24710.11370.1411-0.0045-0.00530.01940.0580.0057-0.0095-0.0646-0.0083-0.01750.3891-0.0062-0.03160.2194-0.01980.159426.71635.970316.2639
71.14670.4432-0.54320.3848-0.27020.27680.03250.1007-0.0008-0.20340.0008-0.11050.01120.0354-0.0240.36540.02180.04950.32430.06650.165229.55913.11634.5282
80.3461-0.22240.03170.4024-0.18260.33530.00330.06760.07060.086-0.0786-0.0341-0.16460.02310.02550.45510.00810.03170.20220.02330.123740.942913.373814.8752
91.10720.87590.2771.55250.32740.4292-0.0146-0.03380.07640.0801-0.0502-0.0297-0.04440.01130.04020.3805-0.0091-0.04440.1380.01870.130738.98541.898723.6443
100.0634-0.1542-0.09150.64690.26840.5323-0.00680.0328-0.00040.1482-0.0279-0.05560.06720.02730.01980.3451-0.01610.02350.1799-0.05980.134540.1391-11.79225.9359
111.09320.5217-0.04371.20940.60490.71560.04050.1064-0.0989-0.0274-0.0142-0.0816-0.02580.04450.02710.41510.0073-0.04970.2228-0.00210.122742.8596-11.504822.4402
120.2893-0.0407-0.07580.06310.04580.1072-0.0081-0.03050.069-0.02150.1166-0.0809-0.040.13050.0686-0.0649-0.01140.04740.0706-0.02950.121952.58511.533260.1937
130.33210.007-0.10670.17920.01680.2370.0778-0.06310.08840.05340.0717-0.0756-0.07310.13730.03940.0298-0.02110.03990.093-0.02420.106247.00424.116859.0031
140.28290.0025-0.16610.13070.00870.29410.1240.07930.15330.00720.01920.0401-0.1798-0.06290.13980.07010.00490.09360.05990.04650.009727.957811.295549.8431
150.65170.0060.11230.2359-0.00370.4033-0.02140.076-0.06-0.05180.03420.07690.0674-0.1583-0.00010.0839-0.03410.00520.1039-0.02980.070526.5142-9.651545.8126
160.81040.1371-0.11041.2096-0.23640.52360.0138-0.0014-0.17230.0051-0.004-0.08780.01240.0904-0.01910.38410.0501-0.02340.26080.00620.200122.976139.16912.4335
170.23590.1234-0.1210.69180.11650.2938-0.03730.11050.0378-0.07750.08820.0460.0395-0.0658-0.04880.3649-0.02820.00150.26890.05390.176814.806949.5593.6063
180.1762-0.17710.06570.4519-0.2030.49220.02820.1136-0.0428-0.1080.0436-0.01020.1445-0.0623-0.05120.3811-0.0319-0.00140.32860.03180.254724.36545.05931.94
190.36530.2655-0.12661.11880.04880.46460.1123-0.094-0.09710.01020.01980.03290.0541-0.0708-0.08820.4207-0.061-0.02430.27090.04760.15769.153242.572217.4478
200.88890.18630.30750.43730.39950.66170.10570.0843-0.2545-0.0757-0.06050.02080.14160.0034-0.02290.4752-0.0394-0.07840.23070.01620.21127.227231.31810.6253
210.65630.38590.19880.51580.04160.50270.1345-0.0398-0.1670.0302-0.0668-0.01250.2367-0.0577-0.02260.5085-0.0294-0.09920.2396-0.01950.1937-6.164131.402617.7834
220.77130.1085-0.08390.6891-0.17060.5879-0.0470.02640.0024-0.0364-0.13060.12110.1154-0.18610.13280.2941-0.04820.02620.2234-0.04870.157-5.817453.022924.2388
230.10540.00410.0466-0.00120.00260.03230.01660.0359-0.1526-0.01550.01750.0750.0666-0.0559-0.0191-0.0577-0.0517-0.07680.07510.03070.131845.445942.882657.0611
240.1229-0.0615-0.01940.27180.00080.0937-0.0431-0.0909-0.00360.08190.0743-0.05610.013-0.0203-0.0325-0.02020.0632-0.04220.02960.00290.061253.652653.128765.6479
250.1188-0.08830.06591.12730.27350.46920.0282-0.0797-0.06630.16370.0339-0.08550.0735-0.0308-0.07860.13170.04860.00170.1370.06670.161249.24647.655974.4856
260.2411-0.02110.020.1414-0.02460.24960.04740.1096-0.0398-0.00940.04260.09410.0612-0.0870.0564-0.0337-0.01-0.03380.05940.01610.09353.427546.370753.1179
270.270.0350.13590.1165-0.03070.08850.0514-0.0349-0.10280.0381-0.0228-0.01740.03990.01-0.04490.1134-0.0644-0.09670.05380.04490.203762.519631.68364.0153
280.1011-0.08540.01060.2426-0.10680.10060.10280.0103-0.1613-0.0165-0.03080.03460.1185-0.0145-0.0930.1332-0.0036-0.14370.0578-0.05560.144171.626331.358355.1923
290.3843-0.26850.00780.24350.07370.21920.10110.104-0.0857-0.00810.0158-0.05980.13190.16420.09130.09120.0781-0.02650.1351-0.07020.067675.132338.456747.7173
300.62410.2899-0.03661.01460.07460.3893-0.03540.20220.0459-0.09820.065-0.0626-0.0940.1626-0.04160.0838-0.01320.00380.21560.01940.063278.132856.233740.0258
310.6529-0.1675-0.33980.04540.1110.34980.00610.03210.1549-0.0153-0.0201-0.0259-0.08040.0932-0.06560.053-0.0161-0.00490.11010.07080.143865.287362.438550.003
321.4716-0.16590.17071.24810.05251.27720.04560.1174-0.0544-0.03580.021-0.1261-0.00750.2481-0.02240.0654-0.0160.01830.16170.03360.100478.918453.320945.3496
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 3 through 27 )A3 - 27
2X-RAY DIFFRACTION2chain 'A' and (resid 28 through 106 )A28 - 106
3X-RAY DIFFRACTION3chain 'A' and (resid 107 through 135 )A107 - 135
4X-RAY DIFFRACTION4chain 'A' and (resid 136 through 155 )A136 - 155
5X-RAY DIFFRACTION5chain 'A' and (resid 156 through 189 )A156 - 189
6X-RAY DIFFRACTION6chain 'A' and (resid 190 through 223 )A190 - 223
7X-RAY DIFFRACTION7chain 'A' and (resid 224 through 246 )A224 - 246
8X-RAY DIFFRACTION8chain 'A' and (resid 247 through 302 )A247 - 302
9X-RAY DIFFRACTION9chain 'A' and (resid 303 through 322 )A303 - 322
10X-RAY DIFFRACTION10chain 'A' and (resid 323 through 366 )A323 - 366
11X-RAY DIFFRACTION11chain 'A' and (resid 367 through 399 )A367 - 399
12X-RAY DIFFRACTION12chain 'B' and (resid 2 through 106 )B2 - 106
13X-RAY DIFFRACTION13chain 'B' and (resid 107 through 246 )B107 - 246
14X-RAY DIFFRACTION14chain 'B' and (resid 247 through 335 )B247 - 335
15X-RAY DIFFRACTION15chain 'B' and (resid 336 through 398 )B336 - 398
16X-RAY DIFFRACTION16chain 'C' and (resid 2 through 63 )C2 - 63
17X-RAY DIFFRACTION17chain 'C' and (resid 64 through 106 )C64 - 106
18X-RAY DIFFRACTION18chain 'C' and (resid 107 through 155 )C107 - 155
19X-RAY DIFFRACTION19chain 'C' and (resid 156 through 209 )C156 - 209
20X-RAY DIFFRACTION20chain 'C' and (resid 210 through 254 )C210 - 254
21X-RAY DIFFRACTION21chain 'C' and (resid 255 through 322 )C255 - 322
22X-RAY DIFFRACTION22chain 'C' and (resid 323 through 398 )C323 - 398
23X-RAY DIFFRACTION23chain 'D' and (resid 3 through 63 )D3 - 63
24X-RAY DIFFRACTION24chain 'D' and (resid 64 through 106 )D64 - 106
25X-RAY DIFFRACTION25chain 'D' and (resid 107 through 135 )D107 - 135
26X-RAY DIFFRACTION26chain 'D' and (resid 136 through 223 )D136 - 223
27X-RAY DIFFRACTION27chain 'D' and (resid 224 through 246 )D224 - 246
28X-RAY DIFFRACTION28chain 'D' and (resid 247 through 283 )D247 - 283
29X-RAY DIFFRACTION29chain 'D' and (resid 284 through 322 )D284 - 322
30X-RAY DIFFRACTION30chain 'D' and (resid 323 through 349 )D323 - 349
31X-RAY DIFFRACTION31chain 'D' and (resid 350 through 376 )D350 - 376
32X-RAY DIFFRACTION32chain 'D' and (resid 377 through 399 )D377 - 399

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