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

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Basic information

Entry
Database: PDB / ID: 6wcs
TitleCrystal structure of Arabidopsis thaliana isochorismoyl-glutamate A pyruvoyl-glutamate lyase in complex with tartrate
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 fungus / regulation of defense response to bacterium / 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
: / Transferase family / Chloramphenicol acetyltransferase-like domain / Chloramphenicol Acetyltransferase / Chloramphenicol acetyltransferase-like domain superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
L(+)-TARTARIC ACID / Protein ENHANCED PSEUDOMONAS SUSCEPTIBILITY 1
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.87 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 31, 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)98,2123
Polymers98,0622
Non-polymers1501
Water5,477304
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2260 Å2
ΔGint-2 kcal/mol
Surface area36280 Å2
Unit cell
Length a, b, c (Å)53.352, 79.432, 194.214
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 214 or resid 225 through 298 or resid 300 through 434))
21(chain B and (resid 4 through 298 or resid 300 through 434))

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
11GLUGLUTHRTHR(chain A and (resid 4 through 214 or resid 225 through 298 or resid 300 through 434))AA4 - 2148 - 218
12ASNASNGLUGLU(chain A and (resid 4 through 214 or resid 225 through 298 or resid 300 through 434))AA225 - 298229 - 302
13PHEPHEVALVAL(chain A and (resid 4 through 214 or resid 225 through 298 or resid 300 through 434))AA300 - 434304 - 438
21GLUGLUGLUGLU(chain B and (resid 4 through 298 or resid 300 through 434))BB4 - 2988 - 302
22PHEPHEVALVAL(chain B and (resid 4 through 298 or resid 300 through 434))BB300 - 434304 - 438

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Components

#1: Protein Protein ENHANCED PSEUDOMONAS SUSCEPTIBILITY 1


Mass: 49030.949 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-TLA / L(+)-TARTARIC ACID


Mass: 150.087 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H6O6
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 304 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 1.87→73.52 Å / Num. obs: 69622 / % possible obs: 99.7 % / Redundancy: 13.1 % / CC1/2: 0.999 / Rmerge(I) obs: 0.089 / Rpim(I) all: 0.026 / Rrim(I) all: 0.094 / Net I/σ(I): 16.9
Reflection shellResolution: 1.87→8.94 Å / Redundancy: 12.6 % / Rmerge(I) obs: 1.785 / Mean I/σ(I) obs: 1.1 / Num. unique obs: 4240 / CC1/2: 0.661 / Rpim(I) all: 0.507 / Rrim(I) all: 0.032 / % possible all: 95.1

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Phasing

PhasingMethod: molecular replacement

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Processing

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

6dd2


Resolution: 1.87→73.52 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 24.29
RfactorNum. reflection% reflection
Rfree0.2256 3416 4.92 %
Rwork0.2025 --
obs0.2036 69495 99.59 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 141.91 Å2 / Biso mean: 48.6745 Å2 / Biso min: 21.36 Å2
Refinement stepCycle: final / Resolution: 1.87→73.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6776 0 14 304 7094
Biso mean--71.31 47.86 -
Num. residues----859
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A2530X-RAY DIFFRACTION10.867TORSIONAL
12B2530X-RAY DIFFRACTION10.867TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 24

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.87-1.890.3931220.31662500262291
1.89-1.920.35751360.292227372873100
1.92-1.950.28471490.271327142863100
1.95-1.980.29761290.255427552884100
1.98-2.020.27041290.258826872816100
2.02-2.050.27611330.255227922925100
2.05-2.090.26431360.245427022838100
2.09-2.140.27571470.238127402887100
2.14-2.180.26921440.230127242868100
2.18-2.230.24881280.231227672895100
2.23-2.290.25351380.234427112849100
2.29-2.350.28311520.2327352887100
2.35-2.420.2411400.236827602900100
2.42-2.50.26421550.235226992854100
2.5-2.590.23371430.225427822925100
2.59-2.690.2271570.226327262883100
2.69-2.810.27381560.233227752931100
2.81-2.960.23771590.215427492908100
2.96-3.150.22191380.20527722910100
3.15-3.390.23581270.211227852912100
3.39-3.730.20791420.18127982940100
3.73-4.270.19051530.162128102963100
4.27-5.380.19441450.157928673012100
5.38-73.520.18951580.192829923150100
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)
11.46270.16370.33051.01850.73380.7770.06480.0058-0.1676-0.01170.0409-0.13230.03290.099-0.00210.3228-0.0013-0.02010.35760.02040.3918-4.5967-29.459117.9222
20.95640.273-0.09271.2898-0.28540.66940.0235-0.06220.0077-0.00980.00020.069-0.0019-0.0411-0.00120.2446-0.0077-0.01120.2992-0.00570.2543-13.5778-16.825416.9866
31.2020.2805-0.36411.28640.01040.9545-0.0326-0.11360.07270.4338-0.125-0.2779-0.12850.2495-0.00810.3769-0.0859-0.10650.43580.01330.340312.959711.33751.5975
41.81250.63670.23781.89150.34841.64630.0625-0.12350.0799-0.0675-0.0651-0.0235-0.0660.00950.00290.3525-0.05020.00370.3142-0.02330.308911.537313.788540.0854
51.07180.2972-0.10410.73780.01990.9166-0.22950.2060.3516-0.62870.15250.165-0.3277-0.0535-0.0110.7297-0.1096-0.04580.44470.06490.4329.355620.766216.0047
60.13620.0357-0.58560.4306-0.19252.6233-0.03280.34470.1767-0.56680.0361-0.1020.22250.71310.48680.7906-0.22370.01310.56430.0970.507518.899520.813716.819
70.05750.09070.03070.44940.30340.3373-0.28330.10960.1766-0.060.06450.4908-0.5161-0.1821-0.01591.0567-0.1726-0.11660.65180.0480.748220.545431.319725.4034
80.74910.67050.35190.68770.03130.8821-0.11050.24490.0642-0.5030.11020.21130.0035-0.1783-0.00140.5321-0.0357-0.05440.4110.01470.39422.428111.669821.581
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid -3 through 41 )A-3 - 41
2X-RAY DIFFRACTION2chain 'A' and (resid 42 through 434 )A42 - 434
3X-RAY DIFFRACTION3chain 'B' and (resid 4 through 25 )B4 - 25
4X-RAY DIFFRACTION4chain 'B' and (resid 26 through 201 )B26 - 201
5X-RAY DIFFRACTION5chain 'B' and (resid 202 through 286 )B202 - 286
6X-RAY DIFFRACTION6chain 'B' and (resid 287 through 333 )B287 - 333
7X-RAY DIFFRACTION7chain 'B' and (resid 334 through 361 )B334 - 361
8X-RAY DIFFRACTION8chain 'B' and (resid 362 through 434 )B362 - 434

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