PDB-3bwb: Crystal structure of the apo form of spermidine synthase from Try...

ID or keywords:

Entry

Database: PDB / ID: 3bwb

Title

Crystal structure of the apo form of spermidine synthase from Trypanosoma cruzi at 2.5 A resolution

Components

Spermidine synthase

Keywords

TRANSFERASE /

Spermidine synthase /

Trypanosoma cruzi / SGPP /

Structural Genomics / PSI /

Protein Structure Initiative / Structural Genomics of Pathogenic Protozoa Consortium

Function / homology

Function and homology information

spermidine synthase /

spermidine synthase activity / polyamine biosynthetic process
Similarity search - Function

Biological species

Trypanosoma cruzi (eukaryote)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 2.5 Å

Authors

Bosch, J. / Hol, W.G.J. / Structural Genomics of Pathogenic Protozoa Consortium (SGPP)

Citation

Journal: To be Published
Title: Crystal structure of spermidine synthase from Trypanosoma cruzi.
Authors: Bosch, J. / Hol, W.G.J.

History

Deposition	Jan 8, 2008	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Apr 1, 2008	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Advisory / Source and taxonomy / Version format compliance

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	3bwb.cif.gz	124.1 KB	Display	PDBx/mmCIF format
PDB format	pdb3bwb.ent.gz	104.9 KB	Display	PDB format
PDBx/mmJSON format	3bwb.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/bw/3bwb ftp://data.pdbj.org/pub/pdb/validation_reports/bw/3bwb	HTTPS FTP

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Related structure data

Related structure data	3bwcC C: citing same article (ref.)
Similar structure data	2pwp-2 3rw9-d 6i1n-2 2hte-1 2hte-2 4tz0-d 3rie-1 4cwa-1 4uoe-1 3i62-d Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search
Other databases	TargetDB: Tcru019078AAA

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Spermidine synthase

B: Spermidine synthase

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

1

Idetical with deposited unit
defined by author&software

Unit cell

Length a, b, c (Å)	43.669, 96.996, 69.649
Angle α, β, γ (deg.)	90.00, 106.33, 90.00
Int Tables number	4
Space group name H-M	P12₁1

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	A
2	1	B
3	1	A
4	1	B

NCS domain segments:

Ens-ID: 1

Dom-ID	Component-ID	Beg label comp-ID	End label comp-ID	Refine code	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	ALA	HIS	3	A	A	31 - 241	31 - 241
2	1	ALA	HIS	3	B	B	31 - 241	31 - 241
3	2	HIS	ILE	1	A	A	241 - 250	241 - 250
4	2	HIS	ILE	1	B	B	241 - 250	241 - 250

#1: Protein	Spermidine synthase / Mass: 34525.773 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Trypanosoma cruzi (eukaryote) / Strain: CL Brener / Gene: Tc00.1047053510339.50 / Plasmid: pET14b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21STAR(DE3) / References: UniProt: Q4DA73, spermidine synthase
#2: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 100 / Source method: isolated from a natural source / Formula: H₂O

#1: Protein

Spermidine synthase /

Mass: 34525.773 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Trypanosoma cruzi (eukaryote) / Strain: CL Brener / Gene: Tc00.1047053510339.50 / Plasmid: pET14b / Production host:

Escherichia coli (E. coli) / Strain (production host): BL21STAR(DE3) / References: UniProt: Q4DA73,

spermidine synthase

#2: Water

ChemComp-HOH / water /

Water

Mass: 18.015 Da / Num. of mol.: 100 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.05 Å³/Da / Density % sol: 40 %
Crystal grow	Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8 Details: 40 % PEG 4000, 6% PEG 20000, 0.1 M Tris-HCl, 0.1 M Potassium phosphate, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 0.97 Å
Detector	Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 25, 2005
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97 Å / Relative weight: 1
Reflection	Resolution: 2.5→20 Å / Num. all: 16956 / Num. obs: 16956 / % possible obs: 87.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.3 % / R_merge(I) obs: 0.07 / R_sym value: 0.081 / Net I/σ(I): 12.23
Reflection shell	Resolution: 2.5→2.6 Å / Redundancy: 2.1 % / R_merge(I) obs: 0.396 / Mean I/σ(I) obs: 3.2 / R_sym value: 0.381 / % possible all: 53.6

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Processing

Software

Name	Version	Classification
REFMAC	5.2.0019	refinement
ADSC	Quantum	data collection
XDS		data reduction
XSCALE		data scaling
SHELXD		phasing

Refinement

Method to determine structure:

SAD / Resolution: 2.5→20 Å / Cor.coef. F_o:F_c: 0.939 / Cor.coef. F_o:F_c free: 0.92 / SU B: 26.28 / SU ML: 0.28 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.351 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.24785	895	5.2 %	RANDOM
R_work	0.19796	-	-	-
obs	0.20068	16306	89.11 %	-
all	-	16306	-	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK

Displacement parameters

B_iso mean: 32.099 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-1.08 Å²	0 Å²	0.19 Å²
2-	-	0.57 Å²	0 Å²
3-	-	-	0.61 Å²

Refinement step

Cycle: LAST / Resolution: 2.5→20 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4500	0	0	100	4600

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.007	0.022	4688
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.02	3232
X-RAY DIFFRACTION	r_angle_refined_deg	1.058	1.96	6372
X-RAY DIFFRACTION	r_angle_other_deg	0.862	3	7870
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	4.954	5	595
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	30.519	23.699	219
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	14.804	15	798
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	14.612	15	33
X-RAY DIFFRACTION	r_chiral_restr	0.068	0.2	693
X-RAY DIFFRACTION	r_gen_planes_refined	0.003	0.02	5248
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	961
X-RAY DIFFRACTION	r_nbd_refined	0.185	0.2	968
X-RAY DIFFRACTION	r_nbd_other	0.18	0.2	3278
X-RAY DIFFRACTION	r_nbtor_refined	0.172	0.2	2216
X-RAY DIFFRACTION	r_nbtor_other	0.08	0.2	2460
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.133	0.2	157
X-RAY DIFFRACTION	r_xyhbond_nbd_other
X-RAY DIFFRACTION	r_metal_ion_refined
X-RAY DIFFRACTION	r_metal_ion_other
X-RAY DIFFRACTION	r_symmetry_vdw_refined	0.109	0.2	17
X-RAY DIFFRACTION	r_symmetry_vdw_other	0.196	0.2	28
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.197	0.2	5
X-RAY DIFFRACTION	r_symmetry_hbond_other
X-RAY DIFFRACTION	r_symmetry_metal_ion_refined
X-RAY DIFFRACTION	r_symmetry_metal_ion_other
X-RAY DIFFRACTION	r_mcbond_it	1.641	4	3697
X-RAY DIFFRACTION	r_mcbond_other	0.209	4	1167
X-RAY DIFFRACTION	r_mcangle_it	1.835	6	4675
X-RAY DIFFRACTION	r_scbond_it	2.293	6	2031
X-RAY DIFFRACTION	r_scangle_it	3.41	10	1683
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Number	Type	Rms dev position (Å)	Weight position
1311	tight positional	0.04	0.05
1453	loose positional	0.65	5
1311	tight thermal	0.05	0.5
1453	loose thermal	1.02	10

LS refinement shell

Resolution: 2.5→2.633 Å / Total num. of bins used: 10

	R_factor	Num. reflection	% reflection
R_free	0.31	86	-
R_work	0.284	1510	-
obs	-	-	57.7 %

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	1.6331	-0.4282	-4.0792	8.075	3.1493	10.7324	-0.1952	0.4186	0.2445	0.1791	0.2473	-0.843	0.5822	0.3557	-0.0521	0.1599	0.0459	-0.0437	0.0123	0.1017	0.3714	10.095	22.1805	13.8823
2	24.5099	9.8219	11.4797	9.2238	4.6125	11.6356	-0.6302	0.7589	0.4512	-0.7683	0.6721	-0.1729	-1.1694	0.5417	-0.0419	0.215	0.0433	0.0406	-0.0068	0.0918	0.3491	9.4715	22.3678	22.3228
3	2.8162	0.0442	0.8749	1.9576	1.9063	2.2717	0.0916	-0.5466	0.3622	0.1068	0.0099	0.0967	-0.0362	-0.0021	-0.1016	0.1163	0.0445	0.0118	0.2434	-0.1033	0.235	11.6366	9.1071	38.4299
4	19.1942	1.9425	-6.3298	31.2058	-0.1377	19.2407	0.6516	-0.9156	1.3843	1.0344	-0.539	-0.3354	-1.505	-0.1722	-0.1126	0.0748	0.0943	0.0238	-0.1856	-0.0939	0.2907	7.2193	24.897	32.9647
5	5.0476	-0.6873	2.8725	5.2047	1.5252	4.6352	-0.1034	-0.2299	0.7409	-0.1118	0.1183	-0.0416	-0.3022	0.2227	-0.0149	0.0579	0.0776	-0.0025	0.204	-0.1634	0.199	17.9959	14.7912	42.5799
6	12.4544	-6.6693	-8.8775	3.5714	4.7539	6.3279	2.1997	5.0501	2.2358	-4.4428	-2.1345	-1.3205	0.3603	-1.3417	-0.0651	1.0636	0.2691	0.1779	1.252	0.1972	0.7334	32.3634	13.2863	32.9294
7	2.6404	-0.3854	0.6243	1.7965	2.1596	3.0586	-0.101	-0.0525	0.1858	0.1064	0.2387	-0.2241	0.0423	0.2	-0.1377	0.0782	0.0393	-0.0412	0.1986	-0.0811	0.2315	22.3652	1.4622	31.9917
8	5.2748	-0.9541	-5.0215	1.9253	2.5424	8.111	-0.1781	-0.0665	-0.511	0.1801	-0.1352	0.1182	0.2639	-0.1213	0.3133	0.1573	0.0071	-0.0161	0.1495	-0.0151	0.1809	12.4623	-4.1386	28.6728
9	4.6437	-0.9312	-5.4723	6.0147	3.3888	11.0381	-0.0154	0.5081	0.6936	-0.5456	0.1409	0.6622	0.3152	-0.66	-0.1255	0.4222	0.1017	-0.0616	0.0743	0.2739	0.1478	9.4322	12.0569	1.0808
10	0.4238	-1.2447	0.2418	3.9213	-1.6353	3.3605	-0.046	0.0111	-0.0385	-0.4533	0.0955	0.0644	-0.3046	-0.4438	-0.0495	0.2599	0.0216	-0.0176	0.4018	0.0965	0.1251	13.2682	2.9747	0.3604
11	2.2735	0.7006	0.4475	1.7636	-0.0569	4.3183	-0.1589	0.5149	-0.5612	-0.3728	-0.1431	-0.044	0.0974	-0.0226	0.302	0.1742	-0.0537	0.061	0.3127	-0.1415	0.2838	9.0733	-17.34	3.0661
12	33.0557	-0.1935	10.8733	7.0679	-4.2778	29.5035	0.0104	1.327	-0.7226	-1.4273	0.5364	0.0759	0.2647	-0.2257	-0.5467	0.1989	-0.0929	0.1238	0.4075	-0.0295	0.0081	14.236	-3.5494	-9.0733
13	7.6191	2.4876	0.0494	5.3806	-1.0693	4.9948	-0.0983	1.075	0.0149	-0.3636	-0.136	0.3945	-0.1216	-0.165	0.2343	0.1414	-0.0437	0.0293	0.3109	-0.2047	0.1487	3.1647	-15.9888	-3.0263
14	3.6228	2.6424	0.8383	4.759	4.3844	5.221	-0.2876	0.4136	0.2221	-0.4204	-0.1402	0.4711	-0.2546	-0.5109	0.4278	0.0959	0.0297	-0.0441	0.3305	-0.1375	0.2832	-5.113	-10.6578	11.2892
15	6.821	2.5673	-0.2968	5.4401	0.715	2.4033	0.0931	0.1277	-0.2547	0.1327	-0.1317	0.1572	-0.0036	-0.085	0.0386	0.1573	0.0352	0.0033	0.2175	-0.0717	0.1548	10.8062	-13.9333	14.7041
16	5.4352	-6.5406	-4.7377	11.8123	7.6928	5.136	-0.4075	-0.2731	-0.2637	0.6573	-0.0255	0.3168	0.4065	-0.1768	0.433	0.1758	-0.0134	0.0184	0.2086	-0.0334	0.2462	4.0164	-7.9143	23.619

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	X-RAY DIFFRACTION	1	A	A	12 - 41	12 - 41
2	X-RAY DIFFRACTION	2	A	A	42 - 72	42 - 72
3	X-RAY DIFFRACTION	3	A	A	73 - 129	73 - 129
4	X-RAY DIFFRACTION	4	A	A	130 - 140	130 - 140
5	X-RAY DIFFRACTION	5	A	A	141 - 179	141 - 179
6	X-RAY DIFFRACTION	6	A	A	180 - 192	180 - 192
7	X-RAY DIFFRACTION	7	A	A	193 - 273	193 - 273
8	X-RAY DIFFRACTION	8	A	A	274 - 302	274 - 302
9	X-RAY DIFFRACTION	9	B	B	16 - 44	16 - 44
10	X-RAY DIFFRACTION	10	B	B	45 - 81	45 - 81
11	X-RAY DIFFRACTION	11	B	B	82 - 129	82 - 129
12	X-RAY DIFFRACTION	12	B	B	130 - 140	130 - 140
13	X-RAY DIFFRACTION	13	B	B	141 - 181	141 - 181
14	X-RAY DIFFRACTION	14	B	B	182 - 240	182 - 240
15	X-RAY DIFFRACTION	15	B	B	241 - 283	241 - 283
16	X-RAY DIFFRACTION	16	B	B	284 - 302	284 - 302

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