PDB-4imb: Structure of strictosidine synthase in complex with 2-(1-methyl-1...

ID or keywords:

Entry

Database: PDB / ID: 4imb

Title

Structure of strictosidine synthase in complex with 2-(1-methyl-1H-indol-3-yl)ethanamine

Components

Strictosidine synthase

Keywords

LYASE/LYASE INHIBITOR /

Strictosidine synthase / strictosidine / LYASE-LYASE INHIBITOR complex

Function / homology

Function and homology information

strictosidine synthase /

strictosidine synthase activity / alkaloid metabolic process /

vacuole / biosynthetic process
Similarity search - Function

Biological species

Rauvolfia serpentina (serpentwood)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.703 Å

Authors

Stoeckigt, J. / Fangrui, W. / Wang, M. / Rajendran, C.

Citation

Journal: Curr.Med.Chem. / Year: 2015
Title: Using Strictosidine Synthase to Prepare Novel Alkaloids.
Authors: Zhu, H. / Kercmar, P. / Wu, F. / Rajendran, C. / Sun, L. / Wang, M. / Stockigt, J.

History

Deposition	Jan 2, 2013	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jan 29, 2014	Provider: repository / Type: Initial release
Revision 1.1	Jun 10, 2015	Group: Database references
Revision 1.2	Dec 16, 2015	Group: Database references
Revision 1.3	Feb 24, 2016	Group: Database references
Revision 1.4	Aug 3, 2016	Group: Database references

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	4imb.cif.gz	242.9 KB	Display	PDBx/mmCIF format
PDB format	pdb4imb.ent.gz	207.7 KB	Display	PDB format
PDBx/mmJSON format	4imb.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	4imb_validation.pdf.gz	311.9 KB	Display	wwPDB validaton report
Full document	4imb_full_validation.pdf.gz	324.7 KB	Display
Data in XML	4imb_validation.xml.gz	24.6 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/im/4imb ftp://data.pdbj.org/pub/pdb/validation_reports/im/4imb	HTTPS FTP

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Related structure data

Related structure data	4iygC C: citing same article (ref.)
Similar structure data	4iyg-2 4bag-2 2fp8-1 4iyg-1 2fpc-2 2fp8-2 2v91-1 4bag-1 6y8g-1 1wb6-2 Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#126 - Jun 2010 Epidermal Growth Factor similarity (1) #259 - Jul 2021 Designed Proteins and Citizen Science similarity (1) #225 - Sep 2018 Phytase similarity (1) #77 - May 2006 Glucose Oxidase similarity (1)

Deposited unit

A: Strictosidine synthase

B: Strictosidine synthase

hetero molecules

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

1

A: Strictosidine synthase

hetero molecules

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

2

B: Strictosidine synthase

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

Unit cell

Length a, b, c (Å)	149.782, 149.782, 121.789
Angle α, β, γ (deg.)	90.00, 90.00, 120.00
Int Tables number	146
Space group name H-M	H3

#1: Protein	Strictosidine synthase / Mass: 33693.602 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rauvolfia serpentina (serpentwood) / Gene: STR1 / Production host: Escherichia coli (E. coli) / References: UniProt: P68175, strictosidine synthase
#2: Chemical	ChemComp-1ES / 2-(1-methyl-1H-indol-3-yl)ethanamine Mass: 174.242 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₁₁H₁₄N₂
#3: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 35 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

Experiment	Method: X-RAY DIFFRACTION

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Sample preparation

Crystal	Density Matthews: 3.9 Å³/Da / Density % sol: 68.47 %

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Data collection

Diffraction source	Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 1 Å
Detector	Type: RAYONIX MX-225 / Detector: CCD / Date: Nov 5, 2011
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 2.7→37.445 Å / Num. all: 27472 / Num. obs: 27432 / Observed criterion σ(I): 2

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Processing

Software

Name: PHENIX / Version: (phenix.refine: 1.8_1069) / Classification: refinement

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.703→37.445 Å / SU ML: 0.43 / σ(F): 2 / Phase error: 31.24 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2726	1371	5 %	0.2726
R_work	0.2082	-	-	-
all	0.2726	27432	-	-
obs	0.2115	27427	98.34 %	-

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 2.703→37.445 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4703	0	13	35	4751

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.009	4847
X-RAY DIFFRACTION	f_angle_d	1.322	6599
X-RAY DIFFRACTION	f_dihedral_angle_d	16.062	1714
X-RAY DIFFRACTION	f_chiral_restr	0.088	714
X-RAY DIFFRACTION	f_plane_restr	0.006	860

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 (%)
2.7028-2.7993	0.4198	137	0.343	2594	X-RAY DIFFRACTION	98
2.7993-2.9114	0.3852	137	0.3207	2615	X-RAY DIFFRACTION	99
2.9114-3.0438	0.3853	137	0.3066	2615	X-RAY DIFFRACTION	99
3.0438-3.2042	0.3396	138	0.2785	2617	X-RAY DIFFRACTION	99
3.2042-3.4049	0.2938	138	0.2341	2634	X-RAY DIFFRACTION	99
3.4049-3.6675	0.2577	138	0.1949	2609	X-RAY DIFFRACTION	99
3.6675-4.0362	0.2555	137	0.176	2611	X-RAY DIFFRACTION	99
4.0362-4.6194	0.2251	137	0.1488	2607	X-RAY DIFFRACTION	99
4.6194-5.8164	0.2232	137	0.1627	2593	X-RAY DIFFRACTION	98
5.8164-37.4491	0.2212	135	0.1802	2561	X-RAY DIFFRACTION	96

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	0.0775	-0.1663	-0.0591	0.1779	0.0531	0.223	0.1132	-0.6329	0.044	-0.1453	-0.0889	-0.6463	-0.0444	-0.5672	0.0005	0.5652	-0.1197	-0.0133	0.5216	0.0786	0.4786	7.0166	34.9718	6.5395
2	1.1108	-0.131	0.6552	0.3017	-0.3189	1.7943	0.173	0.0731	0.0118	0.0236	-0.0273	-0.0799	0.1508	0.0858	0	0.5252	0.029	-0.0212	0.3284	-0.0138	0.4838	22.5784	34.8347	-0.6787
3	0.1601	-0.135	0.0117	0.0728	-0.0197	0.1098	0.1897	0.2992	0.0821	0.6936	-0.2829	-0.602	-0.3237	-0.427	0.0008	0.5736	-0.0172	-0.1054	0.4821	0.0067	0.4575	8.2115	39.5625	-1.5091
4	0.0946	-0.0668	0.1353	0.013	-0.0782	0.1525	0.3932	0.1354	0.1295	0.0923	-0.4887	-0.027	0.2298	-0.1663	-0	0.4866	-0.1412	-0.1022	0.609	-0.0085	0.4541	-8.1045	49.1393	8.1223
5	0.1489	-0.1693	0.0093	0.1593	0.0398	0.1184	0.0923	-0.0011	0.0003	0.045	0.2993	-0.2164	0.4138	-0.4334	0.0004	0.6327	-0.0504	-0.0664	0.881	0.0306	0.593	-5.5627	49.6472	15.4047
6	0.2666	0.0981	0.0857	0.0635	0.0119	0.2498	-0.269	-0.438	-0.2468	0.0553	0.0849	0.1363	-0.4122	-0.6711	0.0001	0.8979	-0.0234	-0.047	0.87	0.1109	0.6986	-14.1871	47.8356	20.6918
7	0.0364	-0.0375	0.0071	0.0281	-0.0084	-0.0205	-0.5019	0.0561	-0.1439	0.1538	0.1508	0.3319	-0.1324	0.1641	-0.0009	1.1696	0.1147	-0.0855	1.0463	0.0467	0.7579	-16.1189	54.1828	24.9133
8	0.2306	-0.1541	0.0612	0.1572	0.0673	0.0557	-0.1886	-0.0756	-0.4207	0.6905	0.2911	-0.0425	-0.5735	-0.4897	-0.0002	1.0148	0.237	0.1509	0.9134	0.1318	0.8393	-26.837	54.8831	17.556
9	0.2337	-0.0834	0.0324	0.0679	-0.098	0.1206	-0.8062	-0.4443	-0.7706	0.4525	0.8256	0.0453	-0.3816	-0.4613	-0.0005	1.1435	0.0767	0.1112	0.9577	0.1089	1.2831	-31.4923	54.6059	16.8187
10	0.257	-0.1316	0.1373	0.0968	0.058	0.129	-0.1169	-0.0188	-0.372	-0.0734	0.0973	1.0655	-0.6481	-0.0741	-0.0011	0.8684	0.1005	-0.0777	0.869	0.0241	0.8731	-31.4618	60.8645	6.694
11	0.1362	-0.0881	0.2118	0.0547	-0.1223	0.1603	0.1156	-0.3457	-0.1404	0.2289	0.3521	-0.0961	0.0159	-0.7046	0.0003	0.6718	-0.0622	-0.1813	0.8536	0.0755	0.6712	-24.9589	56.769	-0.1923
12	0.2419	-0.0048	0.1188	0.0629	-0.0166	0.3058	0.4556	-0.0136	-0.0355	-0.3621	-0.2257	-0.03	0.2535	-0.3401	0.0026	0.853	-0.12	-0.2328	0.7529	0.0185	0.6063	-22.5186	47.8755	-4.5121
13	0.2179	-0.0634	0.0546	0.0599	0.0192	0.1569	0.0473	0.1248	-0.0944	-0.2255	-0.247	-0.2508	0.0977	0.0783	-0.0004	0.5633	-0.1089	-0.054	0.6933	0.0443	0.6128	-11.4236	50.4119	2.1262

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 32 through 72 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 73 through 309 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 310 through 332 )
4	X-RAY DIFFRACTION	4	chain 'B' and (resid 33 through 52 )
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 53 through 82 )
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 83 through 120 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 121 through 139 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 140 through 175 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 176 through 203 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 204 through 243 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 244 through 271 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 272 through 309 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 310 through 333 )

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