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- PDB-6wao: Crystal structure of Arabidopsis thaliana isochorismoyl-glutamate... -

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Entry
Database: PDB / ID: 6wao
TitleCrystal structure of Arabidopsis thaliana isochorismoyl-glutamate A pyruvoyl-glutamate lyase in complex with (2-(3-carboxyphenoxy)acetyl)-L-glutamic acid
ComponentsProtein ENHANCED PSEUDOMONAS SUSCEPTIBILITY 1
KeywordsBIOSYNTHETIC PROTEIN / salicylic acid / BAHD acyltransferase / plant defense metabolism
Function / homology
Function and homology information


regulation of defense response to bacterium / regulation of defense response to fungus / salicylic acid biosynthetic process / response to jasmonic acid / acyltransferase activity / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups / response to bacterium / defense response
Similarity search - Function
Chloramphenicol acetyltransferase-like domain superfamily
Similarity search - Domain/homology
N-[(3-carboxyphenoxy)acetyl]-L-glutamic acid / Protein ENHANCED PSEUDOMONAS SUSCEPTIBILITY 1
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.76 Å
AuthorsTorrens-Spence, M.P. / Weng, J.K.
Funding support United States, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)CHE-1709616 United States
CitationJournal: To Be Published
Title: The structural basis of the isochorismoyl-glutamate pyruvoyl-glutamate lyase activity of Arabidopsis EPS1 in salicylic acid biosynthesis
Authors: Torrens-Spence, M.P. / Weng, J.K.
History
DepositionMar 25, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 4, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: 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: Protein ENHANCED PSEUDOMONAS SUSCEPTIBILITY 1
B: Protein ENHANCED PSEUDOMONAS SUSCEPTIBILITY 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,0384
Polymers97,3872
Non-polymers6512
Water13,619756
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1740 Å2
ΔGint-6 kcal/mol
Surface area34710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.136, 75.353, 193.513
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 4 through 8 or resid 10...
21(chain B and (resid 4 through 8 or resid 10...

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
11GLUGLUILEILE(chain A and (resid 4 through 8 or resid 10...AA4 - 84 - 8
12LYSLYSLEULEU(chain A and (resid 4 through 8 or resid 10...AA10 - 1810 - 18
13SERSERLEULEU(chain A and (resid 4 through 8 or resid 10...AA23 - 6023 - 60
14VALVALALAALA(chain A and (resid 4 through 8 or resid 10...AA62 - 12262 - 122
15GLUGLUVALVAL(chain A and (resid 4 through 8 or resid 10...AA4 - 4344 - 434
16GLUGLUVALVAL(chain A and (resid 4 through 8 or resid 10...AA4 - 4344 - 434
17ALAALALYSLYS(chain A and (resid 4 through 8 or resid 10...AA174 - 181174 - 181
18GLUGLUVALVAL(chain A and (resid 4 through 8 or resid 10...AA4 - 4344 - 434
19GLUGLUVALVAL(chain A and (resid 4 through 8 or resid 10...AA4 - 4344 - 434
110TQGTQGHOHHOH(chain A and (resid 4 through 8 or resid 10...AC - E501 - 601
21GLUGLUILEILE(chain B and (resid 4 through 8 or resid 10...BB4 - 84 - 8
22LYSLYSLEULEU(chain B and (resid 4 through 8 or resid 10...BB10 - 6010 - 60
23VALVALALAALA(chain B and (resid 4 through 8 or resid 10...BB62 - 12262 - 122
24PHEPHEILEILE(chain B and (resid 4 through 8 or resid 10...BB124 - 172124 - 172
25ALAALAVALVAL(chain B and (resid 4 through 8 or resid 10...BB174 - 417174 - 417
26GLUGLUVALVAL(chain B and (resid 4 through 8 or resid 10...BB419 - 434419 - 434
27TQGTQGHOHHOH(chain B and (resid 4 through 8 or resid 10...BD - F501 - 601

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Components

#1: Protein Protein ENHANCED PSEUDOMONAS SUSCEPTIBILITY 1


Mass: 48693.594 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: EPS1, At5g67160, K21H1.12 / Production host: Escherichia coli (E. coli)
References: UniProt: Q9FH97, Transferases; Acyltransferases; Transferring groups other than aminoacyl groups
#2: Chemical ChemComp-TQG / N-[(3-carboxyphenoxy)acetyl]-L-glutamic acid


Mass: 325.271 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H15NO8 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 756 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.06 Å3/Da / Density % sol: 40.4 %
Crystal growTemperature: 300 K / Method: vapor diffusion, hanging drop
Details: 0.2 M Potassium Sodium Tartrate 20 % (w/v) PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97918 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 16, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 1.76→59.45 Å / Num. obs: 81189 / % possible obs: 99.8 % / Redundancy: 13.3 % / CC1/2: 1 / Rmerge(I) obs: 0.063 / Rpim(I) all: 0.018 / Rrim(I) all: 0.066 / Net I/σ(I): 25.6
Reflection shellResolution: 1.76→9.13 Å / Redundancy: 12 % / Rmerge(I) obs: 0.596 / Mean I/σ(I) obs: 3.5 / Num. unique obs: 51695 / CC1/2: 0.924 / Rpim(I) all: 0.257 / Rrim(I) all: 0.65 / % possible all: 96.2

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
Aimlessdata scaling
PHASERphasing
PDB_EXTRACT3.25data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6DD2

6dd2


Resolution: 1.76→59.45 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 21.04 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2118 4099 5.05 %
Rwork0.1724 76996 -
obs0.1744 81095 99.81 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 127.83 Å2 / Biso mean: 31.6723 Å2 / Biso min: 12.75 Å2
Refinement stepCycle: final / Resolution: 1.76→59.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6624 0 70 756 7450
Biso mean--57.38 37.62 -
Num. residues----837
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A2384X-RAY DIFFRACTION7.806TORSIONAL
12B2384X-RAY DIFFRACTION7.806TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 29

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.76-1.780.30181500.25972482263295
1.78-1.80.30921370.233526062743100
1.8-1.820.28961500.233126222772100
1.82-1.850.24081380.209626432781100
1.85-1.870.29541330.189626002733100
1.87-1.90.2051570.186326262783100
1.9-1.930.231170.176626272744100
1.93-1.960.2421510.187126382789100
1.96-1.990.22191360.18326502786100
1.99-2.020.26851260.193526332759100
2.02-2.060.24911210.189626452766100
2.06-2.10.22611260.182326472773100
2.1-2.140.26291290.183726572786100
2.14-2.190.21561430.174226432786100
2.19-2.240.2041480.180426172765100
2.24-2.30.20621400.175126632803100
2.3-2.360.21851260.182226472773100
2.36-2.430.22531580.174726362794100
2.43-2.510.20531430.180826622805100
2.51-2.60.21251500.185426462796100
2.6-2.70.21781520.185326202772100
2.7-2.820.22031220.191626932815100
2.82-2.970.18161540.18326602814100
2.97-3.160.24421250.176827012826100
3.16-3.40.2081590.175726812840100
3.4-3.740.19561460.153127022848100
3.74-4.280.19071480.139127132861100
4.29-5.40.18191370.140327602897100
5.4-59.450.20051770.174328763053100
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)
12.1533-0.59850.67732.2033-0.37131.12380.07480.1305-0.24030.0424-0.15040.10980.10080.08090.07540.1442-0.04590.00470.16540.00290.19014.5498-28.4266-20.5401
21.0656-0.1852-0.17081.57440.17041.33340.01520.0746-0.0984-0.0067-0.03520.06380.0746-0.06370.01360.1347-0.05-0.00460.1123-0.00690.14885.3252-26.7471-20.4412
31.269-0.62650.45531.93630.16770.6910.1071-0.10560.01370.2277-0.1456-0.01260.00130.20970.07830.147-0.0277-0.03430.1690.00160.147615.8181-7.0812-11.8226
40.95380.39830.50171.11650.56340.6446-0.020.0122-0.0430.06580.0325-0.14760.03710.0785-0.00120.1476-0.0148-0.00630.16830.00380.187518.9325-10.7822-13.9203
51.1043-0.79460.27141.36010.05741.40090.08260.31970.0251-0.0421-0.09320.1172-0.119-0.3172-0.00560.14930.0326-0.00390.26260.02650.1915-12.820813.792-41.8704
61.5602-0.47920.15871.3225-0.11212.16770.16020.30810.0658-0.0887-0.1549-0.014-0.0235-0.14880.0060.13130.0361-0.01010.21330.02070.1236-10.150112.5147-41.1208
71.7189-1.1253-0.63283.1542-0.17062.0516-0.0610.1373-0.18070.00240.09320.67050.056-0.9212-0.14650.29150.0179-0.09360.592-0.02820.3565-30.918416.9316-37.9518
81.9686-0.84640.2661.6083-0.15441.94560.0458-0.15870.04380.2918-0.04570.044-0.13580.1845-0.02730.241-0.0617-0.00830.0956-0.06080.1381-9.835414.8654-14.9701
93.14631.3920.82193.25291.98623.3212-0.01060.02930.19170.02470.1133-0.1557-0.2090.2355-0.12570.1781-0.01910.04160.1544-0.03010.1584-9.190322.9647-12.6676
102.25180.57022.19950.60521.09794.22480.0772-0.06540.08120.0487-0.0660.084-0.0349-0.2992-0.00760.2140.00870.02030.2055-0.02840.2314-21.267420.0362-17.5487
113.4552-2.47620.41851.95620.16952.2458-0.0120.15570.305-0.0797-0.17920.0074-0.4093-0.16510.20090.2436-0.0001-0.00980.2485-0.01240.2156-20.526423.0285-25.6212
122.31391.28810.67873.09342.8415.5380.14730.07480.04280.0071-0.0561-0.21150.0930.0783-0.09330.08480.0318-0.02280.1390.02080.1418-5.47646.9523-31.3039
132.099-0.79430.84152.40920.69314.38450.0743-0.0367-0.05720.26570.2018-0.34960.32840.4276-0.14780.1931-0.014-0.01670.2008-0.05930.1924-1.038913.2964-15.8054
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 4 through 52 )A4 - 52
2X-RAY DIFFRACTION2chain 'A' and (resid 53 through 211 )A53 - 211
3X-RAY DIFFRACTION3chain 'A' and (resid 212 through 254 )A212 - 254
4X-RAY DIFFRACTION4chain 'A' and (resid 255 through 434 )A255 - 434
5X-RAY DIFFRACTION5chain 'B' and (resid 4 through 52 )B4 - 52
6X-RAY DIFFRACTION6chain 'B' and (resid 53 through 180 )B53 - 180
7X-RAY DIFFRACTION7chain 'B' and (resid 181 through 208 )B181 - 208
8X-RAY DIFFRACTION8chain 'B' and (resid 209 through 254 )B209 - 254
9X-RAY DIFFRACTION9chain 'B' and (resid 255 through 286 )B255 - 286
10X-RAY DIFFRACTION10chain 'B' and (resid 287 through 333 )B287 - 333
11X-RAY DIFFRACTION11chain 'B' and (resid 334 through 374 )B334 - 374
12X-RAY DIFFRACTION12chain 'B' and (resid 375 through 394 )B375 - 394
13X-RAY DIFFRACTION13chain 'B' and (resid 395 through 434 )B395 - 434

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