PDB-27lj: the structure of cis-isoeugenol synthase AtaIGS1 mutant

ID or keywords:

Entry

Database: PDB / ID: 27lj

Title

the structure of cis-isoeugenol synthase AtaIGS1 mutant

Components

Isoeugenol synthase 1

Keywords

PLANT PROTEIN / cis-isoeugenol synthase / short-chain dehydrogenases/reductases

Function / homology

: / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / DI(HYDROXYETHYL)ETHER

Function and homology information

Biological species

Acorus tatarinowii (plant)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.89718509336 Å

Authors

Long, G.F. / Wang, G.Q.

Funding support

1items

Citation

Journal: To Be Published
Title: Structural basis for cis-phenylpropene biosynthesis by dual conformational selection of substrate and reaction intermediate
Authors: Long, G.F. / Wang, G.Q.

History

Deposition	Jun 4, 2026	Deposition site: PDBJ / Processing site: PDBC
Revision 1.0	Jun 24, 2026	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	27lj.cif.gz	321.3 KB	Display	PDBx/mmCIF format
PDB format	pdb27lj.ent.gz		Display	PDB format
PDBx/mmJSON format	27lj.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/7l/27lj ftp://data.pdbj.org/pub/pdb/validation_reports/7l/27lj	HTTPS FTP

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Related structure data

Related structure data	27hoC C: citing same article (ref.)
Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Isoeugenol synthase 1

B: Isoeugenol synthase 1

hetero molecules

72.1 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Isoeugenol synthase 1

hetero molecules

defined by author&software
36.1 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: Isoeugenol synthase 1

hetero molecules

defined by author&software
36 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	41.264, 177.570, 71.530
Angle α, β, γ (deg.)	90.000, 94.060, 90.000
Int Tables number	4
Space group name H-M	P12₁1
Space group name Hall	P2yb
Symmetry operation	#1: x,y,z #2: -x,y+1/2,-z

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID
1	1
2	1

NCS domain segments:

Ens-ID: 1 / Beg auth comp-ID: GLY / Beg label comp-ID: GLY / End auth comp-ID: PRO / End label comp-ID: PRO / Auth seq-ID: 3 - 308 / Label seq-ID: 6 - 311

Dom-ID	Component-ID	Selection details	Auth asym-ID	Label asym-ID
1	1	chain 'A'	A	A
2	2	chain 'B'	B	B

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Protein , 1 types, 2 molecules AB

#1: Protein	Isoeugenol synthase 1 Mass: 34886.109 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Acorus tatarinowii (plant) / Production host: Rosetta (plant)

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Non-polymers , 7 types, 573 molecules

#2: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Cl / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical	ChemComp-PEG / DI(HYDROXYETHYL)ETHER Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₄H₁₀O₃ / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical	ChemComp-NA / SODIUM ION Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical	ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE Mass: 743.405 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₂₁H₂₈N₇O₁₇P₃ / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical	ChemComp-A1FAW / 2-(2-methylphenyl)ethanol Mass: 136.191 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₉H₁₂O / Feature type: SUBJECT OF INVESTIGATION
#7: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₂H₆O₂ / Feature type: SUBJECT OF INVESTIGATION
#8: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 556 / Source method: isolated from a natural source / Formula: H₂O

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Details

Has ligand of interest	Y
Has protein modification	N

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 3.75 Å³/Da / Density % sol: 67.17 %
Crystal grow	Temperature: 289.2 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 10% PEG 20 000, 20% PEG MME 550, 0.03 M of each NPS, 0.1 M bicine/Trizma base pH 8.5

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.979 Å
Detector	Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Dec 26, 2022
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.979 Å / Relative weight: 1
Reflection	Resolution: 1.897→55.58 Å / Num. obs: 80536 / % possible obs: 100 % / Redundancy: 6.6 % / CC_1/2: 0.994 / Net I/σ(I): 6.9
Reflection shell	Resolution: 1.9→1.95 Å / Num. unique obs: 5960 / CC_1/2: 0.623

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Processing

Software

Name	Version	Classification
PHENIX	1.12_2829	refinement
PHENIX	1.12_2829	refinement
DIALS		data reduction
DIALS		data scaling
PHENIX		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.89718509336→41.1601468669 Å / SU ML: 0.215389100546 / Cross valid method: FREE R-VALUE / σ(F): 1.46525289055 / Phase error: 20.6840461827
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2

	R_factor	Num. reflection	% reflection
R_free	0.191624618035	1988	2.47079294059 %
R_work	0.167719585289	78472	-
obs	0.168308682696	80460	99.5545657016 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL

Displacement parameters

B_iso mean: 35.4086891538 Å²

Refinement step

Cycle: LAST / Resolution: 1.89718509336→41.1601468669 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4808	0	138	556	5502

Refine LS restraints

Type: f_bond_d / Dev ideal: 0.0185841129091 / Number: 5027

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
1.8972-1.9446	0.35142346135	134	0.30191147036	5330	X-RAY DIFFRACTION	94.6147186147
1.9446-1.9972	0.300187602602	145	0.269905281137	5585	X-RAY DIFFRACTION	99.9128160418
1.9972-2.056	0.24792748912	146	0.235376990798	5656	X-RAY DIFFRACTION	99.9138970208
2.056-2.1223	0.239359888575	132	0.210364550263	5581	X-RAY DIFFRACTION	99.9300332342
2.1223-2.1982	0.225473127647	147	0.187146252369	5621	X-RAY DIFFRACTION	100
2.1982-2.2862	0.209924121103	140	0.179524949033	5652	X-RAY DIFFRACTION	99.982737787
2.2862-2.3902	0.236322689103	149	0.173686739113	5583	X-RAY DIFFRACTION	100
2.3902-2.5162	0.19717240086	139	0.163955221434	5608	X-RAY DIFFRACTION	99.9130737135
2.5162-2.6738	0.213878766057	145	0.165475705324	5625	X-RAY DIFFRACTION	99.9826719806
2.6738-2.8802	0.169505548555	139	0.160924188363	5633	X-RAY DIFFRACTION	99.9826779837
2.8802-3.17	0.204268436078	137	0.161698203878	5671	X-RAY DIFFRACTION	100
3.17-3.6285	0.168928012135	150	0.150174809804	5605	X-RAY DIFFRACTION	99.9305434971
3.6285-4.5705	0.145489688361	146	0.131428913927	5659	X-RAY DIFFRACTION	99.9655588083

Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

ID	L11 (°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)
1	0.336215600402	-0.280638412921	-0.0657360200409	0.341992015272	0.319217420785	0.443601530264	-0.166377594722	-0.229310655181	0.0471589952077	0.414276569525	0.21030141975	-0.116926972091	0.0225736322403	0.18112320041	0.0232073089569	0.38763700941	0.0501465857859	-0.0274899729405	0.28222945023	0.0112270932761	0.178561080185	-0.0017987696449	9.30136871577	29.2340546028
2	0.477412423873	-0.167711736378	0.231863524361	0.489940388719	0.161288277801	0.379391502891	0.0222088432296	-0.0977827990362	-0.00655186147521	0.0180808216684	-0.0453342611621	0.0819462605833	-0.0793573116913	-0.0160055984061	-1.53916860738E-5	0.18790914589	-0.00479080152414	0.0138136087238	0.191332394828	-0.011011238382	0.182894453813	-11.8656666117	7.51090313946	16.0441257977
3	0.0503276265628	0.00826765362913	0.0297927292391	0.0968004657525	0.0609533363319	0.00626069316639	0.0653000953415	-0.0591386615152	-0.138881411813	0.156408220047	-0.107023213339	0.135233689145	0.0691794496723	-0.00775057957401	0.000224044236139	0.164306665411	0.0040629254831	0.0133706554798	0.223186033015	0.0233782686042	0.211193008863	6.86675865404	-16.747975914	17.7575755359
4	0.37291109395	0.0145517506904	0.0712120332142	0.209694395871	-0.302413066965	0.11344048791	0.00357677138045	0.0385527066994	-0.062130090581	-0.0626527770738	-0.0287548696821	-0.157704193615	-0.0618347223427	0.0275282072505	-2.05204405276E-5	0.171980695284	0.00157398250579	-0.00291028184352	0.175451400391	0.0082553191065	0.179534877071	5.60796910563	-1.62154432117	7.929129311
5	0.673280178026	-0.215880000647	0.00830070223172	0.850375576953	-0.245077714389	0.196687585513	-0.0582605337764	-0.0423477792395	-0.358901699184	-0.0975203671341	0.150542914444	0.190012763612	-0.0394814905447	-0.0957346095393	0.0435632199037	0.168082767427	0.0227262432474	-0.00310100721907	0.191345131662	0.0468703334321	0.32649493328	-3.09933929546	-14.4522194577	9.3510140642
6	0.194172147752	-0.0679573358573	-0.0128593236167	0.00598431282998	0.0293723789347	0.136537446061	-0.0392491200565	-0.0532905252858	0.00523636106523	-0.144897562734	0.0304105001834	-0.273055114871	-0.0127631499405	0.0167381109837	0.000108833393689	0.177825953468	-0.0173374095629	0.00497943259807	0.243352607641	0.0377002842663	0.270756965853	13.1562383358	0.368361535338	11.5163536187
7	0.660872464536	-0.0770469559934	-0.00503416916462	0.586966077426	0.407939708169	1.19658844138	0.0676789260043	0.110480215291	-0.170935245039	-0.280071843874	-0.0974351637366	0.231399679277	0.0181974772754	-0.11647506275	0.0119489034175	0.249390672594	0.006906419153	-0.0425049969731	0.211435723423	-0.0534014305956	0.180514969016	-12.3929310633	21.2410912309	-23.85879987
8	0.121469706833	-0.152773100262	-0.1790144565	0.31504703614	0.0756852009659	0.138899670695	-0.0248655817322	0.0224729303226	-0.0461916616544	-0.0207812796748	0.0520965934132	0.189695727117	0.0388679822409	-0.0328697453586	1.7395074432E-5	0.169745206884	-0.0196955243147	0.0185671011854	0.184433515878	0.0126132351902	0.184968049812	-14.2820989849	30.5444302251	-6.70415092771
9	0.584133815225	0.209497517204	0.216286100262	0.223406416196	0.01155340589	-0.041854101961	-0.0445068260439	0.0886349073389	0.132072637819	0.037859374766	-0.0268867388086	-0.0981763879493	0.00989465180821	0.0203359314621	-0.000117975998747	0.172139446963	-0.0102648025447	0.00843686814114	0.200198358534	-0.00442114699835	0.173588263788	0.862191084418	42.0471512435	-14.9984507555
10	0.504913660025	0.0342965359858	-0.102293016097	0.437809388009	-0.00668893281306	0.189317847336	0.0353595263017	-0.0750232024135	0.200893560034	0.0342911150608	-0.0186259214175	0.0292805360125	0.0203774639157	0.0147211656264	-1.41930800766E-5	0.170722100438	-0.0121688468912	-0.0134734538372	0.176233972052	0.0124764073856	0.241215323418	-1.14039658389	43.1234067994	-9.84232995108
11	0.115121056197	0.0954233929749	-0.0496201592932	0.0552032160603	-0.0331447002077	0.0896011781285	0.0122461393618	-0.136467010737	0.113711264076	0.187962837726	0.0291999752004	0.0658096218461	0.0454510943253	-0.178360669515	3.17809839243E-5	0.23242587934	-0.0247446834553	0.000357997018743	0.229151473591	0.00325766630615	0.193566030536	-5.92881661356	39.452079909	-4.01792478339
12	-0.00447804196916	0.0505295698432	0.0300714232402	0.0680699125008	-0.00193021896004	0.0828414035408	-0.100073204327	-0.00312567189259	-0.195418853322	-0.0510259581424	-0.00933149301604	-0.556882417784	0.00918006337129	0.0487259560684	0.000362794888855	0.185841676508	-0.00460623641727	0.0312478775692	0.227005383664	0.015070585062	0.311820351505	8.90950124586	32.290489122	-14.6605075699

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 3 through 68 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 69 through 157 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 158 through 178 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 179 through 233 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 234 through 284 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 285 through 308 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 3 through 111 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 112 through 157 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 158 through 200 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 201 through 257 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 258 through 284 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 285 through 308 )

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