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- PDB-5oe4: Crystal structure of the N-terminal domain of PqsA in complex wit... -

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Basic information

Entry
Database: PDB / ID: 5oe4
TitleCrystal structure of the N-terminal domain of PqsA in complex with anthraniloyl-AMP (crystal form 2)
ComponentsAnthranilate--CoA ligase
KeywordsLIGASE / PQS / PqsA / Anthranilate / Anthraniloyl-AMP / Anthraniloyl-CoA / Pseudomonas Quinolone Signal / Pseudomonas aeruginosa / Quorum Sensing / Aryl-CoA ligase / ANL superfamily
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
Chem-3UK / Anthranilate--CoA ligase
Similarity search - Component
Biological speciesPseudomonas aeruginosa PAO1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.904 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
Revision 1.2Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,7234
Polymers88,7902
Non-polymers9332
Water12,773709
1
A: Anthranilate--CoA ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,8622
Polymers44,3951
Non-polymers4661
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Anthranilate--CoA ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,8622
Polymers44,3951
Non-polymers4661
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)77.798, 71.966, 84.417
Angle α, β, γ (deg.)90.000, 116.900, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 2 through 12 or resid 14...
21(chain B and (resid 2 through 12 or resid 14...

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11SERSERPHEPHE(chain A and (resid 2 through 12 or resid 14...AA2 - 122 - 12
12LEULEUPROPRO(chain A and (resid 2 through 12 or resid 14...AA14 - 1814 - 18
13THRTHRPROPRO(chain A and (resid 2 through 12 or resid 14...AA20 - 6420 - 64
14LEULEUPROPRO(chain A and (resid 2 through 12 or resid 14...AA66 - 8566 - 85
15SERSERSERSER(chain A and (resid 2 through 12 or resid 14...AA8787
16GLUGLUALAALA(chain A and (resid 2 through 12 or resid 14...AA89 - 9189 - 91
17ALAALACYSCYS(chain A and (resid 2 through 12 or resid 14...AA93 - 9993 - 99
18ALAALAARGARG(chain A and (resid 2 through 12 or resid 14...AA101 - 106101 - 106
19PROPROHISHIS(chain A and (resid 2 through 12 or resid 14...AA119 - 151119 - 151
110GLNGLNALAALA(chain A and (resid 2 through 12 or resid 14...AA153 - 158153 - 158
111PHEPHETHRTHR(chain A and (resid 2 through 12 or resid 14...AA160 - 164160 - 164
112PROPROASPASP(chain A and (resid 2 through 12 or resid 14...AA171 - 199171 - 199
113LEULEUPHEPHE(chain A and (resid 2 through 12 or resid 14...AA201 - 208201 - 208
114GLYGLYTHRTHR(chain A and (resid 2 through 12 or resid 14...AA210 - 232210 - 232
115PROPROPHEPHE(chain A and (resid 2 through 12 or resid 14...AA234 - 246234 - 246
116PROPROGLUGLU(chain A and (resid 2 through 12 or resid 14...AA248 - 296248 - 296
117CYSCYSGLYGLY(chain A and (resid 2 through 12 or resid 14...AA298 - 346298 - 346
118GLNGLNSERSER(chain A and (resid 2 through 12 or resid 14...AA348 - 366348 - 366
119GLUGLUPHEPHE(chain A and (resid 2 through 12 or resid 14...AA368 - 384368 - 384
120ARGARGASPASP(chain A and (resid 2 through 12 or resid 14...AA386 - 387386 - 387
121SERSERGLUGLU(chain A and (resid 2 through 12 or resid 14...AA389 - 398389 - 398
21SERSERPHEPHE(chain B and (resid 2 through 12 or resid 14...BB2 - 122 - 12
22LEULEUPROPRO(chain B and (resid 2 through 12 or resid 14...BB14 - 1814 - 18
23THRTHRPROPRO(chain B and (resid 2 through 12 or resid 14...BB20 - 6420 - 64
24LEULEUPROPRO(chain B and (resid 2 through 12 or resid 14...BB66 - 8566 - 85
25SERSERSERSER(chain B and (resid 2 through 12 or resid 14...BB8787
26GLUGLUALAALA(chain B and (resid 2 through 12 or resid 14...BB89 - 9189 - 91
27ALAALACYSCYS(chain B and (resid 2 through 12 or resid 14...BB93 - 9993 - 99
28ALAALAARGARG(chain B and (resid 2 through 12 or resid 14...BB101 - 106101 - 106
29PROPROPROPRO(chain B and (resid 2 through 12 or resid 14...BB111111
210LEULEUHISHIS(chain B and (resid 2 through 12 or resid 14...BB120 - 151120 - 151
211GLNGLNALAALA(chain B and (resid 2 through 12 or resid 14...BB153 - 158153 - 158
212PHEPHEASPASP(chain B and (resid 2 through 12 or resid 14...BB160 - 199160 - 199
213LEULEUPHEPHE(chain B and (resid 2 through 12 or resid 14...BB201 - 208201 - 208
214GLYGLYTHRTHR(chain B and (resid 2 through 12 or resid 14...BB210 - 232210 - 232
215PROPROPHEPHE(chain B and (resid 2 through 12 or resid 14...BB234 - 246234 - 246
216PROPROGLUGLU(chain B and (resid 2 through 12 or resid 14...BB248 - 296248 - 296
217CYSCYSGLYGLY(chain B and (resid 2 through 12 or resid 14...BB298 - 346298 - 346
218GLNGLNSERSER(chain B and (resid 2 through 12 or resid 14...BB348 - 366348 - 366
219GLUGLUPHEPHE(chain B and (resid 2 through 12 or resid 14...BB368 - 384368 - 384
220ARGARGASPASP(chain B and (resid 2 through 12 or resid 14...BB386 - 387386 - 387
221SERSERGLUGLU(chain B and (resid 2 through 12 or resid 14...BB389 - 398389 - 398

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Components

#1: Protein Anthranilate--CoA ligase


Mass: 44395.195 Da / Num. of mol.: 2
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-3UK / 5'-O-[(S)-[(2-aminobenzoyl)oxy](hydroxy)phosphoryl]adenosine


Mass: 466.342 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H19N6O8P / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 709 / 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: 2.37 Å3/Da / Density % sol: 48.18 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.8
Details: 100 mM tri-sodium citrate (pH 5.8), 240 mM ammonium acetate, 22.5% PEG3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Feb 23, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→42.355 Å / Num. obs: 65199 / % possible obs: 99.9 % / Redundancy: 6.7 % / Biso Wilson estimate: 18.27 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.152 / Rpim(I) all: 0.064 / Rrim(I) all: 0.165 / Net I/σ(I): 10.6
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsCC1/2Rpim(I) allRrim(I) all% possible all
1.9-1.956.71.0610.7240.441.1599.9
8.93-42.356.90.0270.9990.0110.02999.1

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
Aimless0.5.31data scaling
MOLREPphasing
PHENIX1.12rc2_2821refinement
PDB_EXTRACT3.22data extraction
XDSdata reduction
Coot0.8.8model building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2V7B

2v7b


Resolution: 1.904→42.355 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 26.85
RfactorNum. reflection% reflection
Rfree0.2501 3151 4.84 %
Rwork0.2091 --
obs0.211 65168 99.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 95.37 Å2 / Biso mean: 27.8866 Å2 / Biso min: 8.79 Å2
Refinement stepCycle: final / Resolution: 1.904→42.355 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5934 0 102 709 6745
Biso mean--20 27.54 -
Num. residues----771
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0046347
X-RAY DIFFRACTIONf_angle_d0.6328661
X-RAY DIFFRACTIONf_chiral_restr0.041934
X-RAY DIFFRACTIONf_plane_restr0.0041185
X-RAY DIFFRACTIONf_dihedral_angle_d12.783837
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A4130X-RAY DIFFRACTION6.632TORSIONAL
12B4130X-RAY DIFFRACTION6.632TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 23 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.904-1.93240.32391290.31226792808
1.9324-1.96260.32311150.290327292844
1.9626-1.99480.3121510.281526682819
1.9948-2.02920.31491490.275526332782
2.0292-2.06610.27571280.261227212849
2.0661-2.10580.2971300.263126962826
2.1058-2.14880.29451340.245926472781
2.1488-2.19550.27231400.253626862826
2.1955-2.24660.29791330.24626992832
2.2466-2.30280.31591470.257126612808
2.3028-2.3650.28391410.235327142855
2.365-2.43460.26951570.218126342791
2.4346-2.51320.24511480.210526832831
2.5132-2.6030.24681520.213926922844
2.603-2.70720.28641380.213826862824
2.7072-2.83040.23951480.219526832831
2.8304-2.97960.29621250.203627042829
2.9796-3.16620.25121430.206927032846
3.1662-3.41060.241340.188227182852
3.4106-3.75360.23411360.176726952831
3.7536-4.29630.18681010.167127632864
4.2963-5.41110.16691250.141327372862
5.4111-42.36540.19981470.189227862933
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)
10.1407-0.1842-0.11060.26920.15950.13280.1452-0.01970.0139-0.21160.0164-0.2169-0.0031-0.0620.08860.2615-0.08980.07020.15290.02390.168218.770229.57283.5462
20.07890.0146-0.02730.0086-0.00850.0586-0.05260.039-0.0091-0.14790.0187-0.1356-0.04280.0411-0.25710.3655-0.04020.11080.11240.04970.156510.474134.4220.3169
30.2372-0.1658-0.11950.41080.02880.2234-0.0040.10240.0643-0.0768-0.08930.2433-0.0615-0.1532-0.12370.2615-0.00070.04170.1683-0.00490.1476-1.212726.084.9706
40.2166-0.0698-0.06460.3190.06020.1966-0.00770.00980.0042-0.0141-0.0136-0.1739-0.11360.0677-0.0150.1626-0.02630.01470.14030.0170.149614.760320.24879.7051
50.10980.20080.0640.4512-0.00960.3163-0.09350.1801-0.1118-0.39490.1468-0.29340.02690.06720.08270.2994-0.03650.12720.1768-0.02820.171417.00837.513-4.7052
60.29930.1695-0.03650.2218-0.04520.01030.0108-0.0972-0.1935-0.00910.0655-0.09360.0702-0.02110.27860.07150.0199-0.03170.15770.01280.221322.07014.28379.4839
70.2107-0.14420.01160.80670.26430.14570.0306-0.1721-0.16180.4886-0.048-0.05130.1348-0.0866-0.1610.2299-0.0154-0.06040.16140.0680.232416.40961.675921.5347
80.2925-0.0959-0.20950.45260.18960.2212-0.00910.0365-0.15840.1367-0.00720.12420.0103-0.1109-0.00150.26040.00570.07030.14160.01130.145625.135822.8698-36.6682
90.3785-0.11060.11520.8876-0.25070.2389-0.0893-0.07620.01320.35660.0987-0.0026-0.0744-0.0330.02930.24940.02620.02020.14190.00750.126330.843138.8892-25.2957
100.2413-0.0512-0.05420.88920.31680.3964-0.01260.14630.1701-0.2348-0.0159-0.3167-0.24280.06830.02080.148-0.0386-0.00430.13810.01880.22546.149948.9856-37.5327
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 27 )A2 - 27
2X-RAY DIFFRACTION2chain 'A' and (resid 28 through 48 )A28 - 48
3X-RAY DIFFRACTION3chain 'A' and (resid 49 through 145 )A49 - 145
4X-RAY DIFFRACTION4chain 'A' and (resid 146 through 209 )A146 - 209
5X-RAY DIFFRACTION5chain 'A' and (resid 210 through 302 )A210 - 302
6X-RAY DIFFRACTION6chain 'A' and (resid 303 through 322 )A303 - 322
7X-RAY DIFFRACTION7chain 'A' and (resid 323 through 398 )A323 - 398
8X-RAY DIFFRACTION8chain 'B' and (resid 2 through 145 )B2 - 145
9X-RAY DIFFRACTION9chain 'B' and (resid 146 through 322 )B146 - 322
10X-RAY DIFFRACTION10chain 'B' and (resid 323 through 398 )B323 - 398

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