PDB-3n29: Crystal structure of carboxynorspermidine decarboxylase complexed...

ID or keywords:

Entry

Database: PDB / ID: 3n29

Title

Crystal structure of carboxynorspermidine decarboxylase complexed with Norspermidine from Campylobacter jejuni

Components

Carboxynorspermidine decarboxylase

Keywords

LYASE

Function / homology

Function and homology information

carboxynorspermidine decarboxylase / nor-spermidine biosynthetic process / spermidine biosynthetic process / carboxy-lyase activity / pyridoxal phosphate binding / protein homodimerization activity / cytoplasm
Similarity search - Function

Biological species

Campylobacter jejuni subsp. jejuni 81116 (Campylobacter)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 1.9 Å

Authors

Deng, X. / Lee, J. / Michael, A.J. / Tomchick, D.R. / Goldsmith, E.J. / Phillips, M.A.

Citation

Journal: J.Biol.Chem. / Year: 2010
Title: Evolution of substrate specificity within a diverse family of beta/alpha-barrel-fold basic amino acid decarboxylases: X-ray structure determination of enzymes with specificity for L-arginine ...
Authors: Deng, X. / Lee, J. / Michael, A.J. / Tomchick, D.R. / Goldsmith, E.J. / Phillips, M.A.

History

Deposition	May 17, 2010	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jun 9, 2010	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Advisory / Refinement description / Version format compliance
Revision 1.2	Feb 22, 2012	Group: Database references

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	3n29.cif.gz	164.6 KB	Display	PDBx/mmCIF format
PDB format	pdb3n29.ent.gz	138.1 KB	Display	PDB format
PDBx/mmJSON format	3n29.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	3n29_validation.pdf.gz	484 KB	Display	wwPDB validaton report
Full document	3n29_full_validation.pdf.gz	492.9 KB	Display
Data in XML	3n29_validation.xml.gz	32.6 KB	Display
Data in CIF	3n29_validation.cif.gz	46.9 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/n2/3n29 ftp://data.pdbj.org/pub/pdb/validation_reports/n2/3n29	HTTPS FTP

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Related structure data

Related structure data	3n2oC C: citing same article (ref.)
Similar structure data	1n4p-2 3mt1-d 5wfn-2 1r0e-d 2hyi-1 1249 2pvz-d 1n4s-3 1n4r-2 2yxx-2 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

Deposited unit

A: Carboxynorspermidine decarboxylase

B: Carboxynorspermidine decarboxylase

hetero molecules

95.7 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)	144.498, 144.498, 79.901
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	96
Space group name H-M	P4₃2₁2

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	2	A
2	2	B

#1: Protein	Carboxynorspermidine decarboxylase Mass: 47458.078 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Campylobacter jejuni subsp. jejuni 81116 (Campylobacter) Strain: strain 81116 Gene: carboxynorspermidine decarboxylase, CJJHB9313_1507, nspC Plasmid: PET100 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: A3ZCM2, UniProt: A8FNH9*PLUS
#2: Chemical	ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate Mass: 247.142 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₈H₁₀NO₆P
#3: Chemical	ChemComp-NSD / N-(3-aminopropyl)propane-1,3-diamine Mass: 131.219 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₆H₁₇N₃ / Comment: medication*YM
#4: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₃H₈O₃
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 384 / 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: 2.2 Å³/Da / Density % sol: 44.02 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 2.75 M AmSO4, 0.1 M BICINE pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97948 Å
Detector	Type: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 20, 2009
Radiation	Monochromator: Rosenbaum-Rock high-resolution double-crystal monochromator. Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97948 Å / Relative weight: 1
Reflection	Resolution: 1.9→102.06 Å / Num. all: 66838 / Num. obs: 66670 / % possible obs: 99.8 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / R_merge(I) obs: 0.136
Reflection shell	Resolution: 1.9→1.95 Å / % possible all: 98.2

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Processing

Software

Name	Version	Classification
HKL-3000		data collection
SHELXD		phasing
REFMAC	5.5.0072	refinement
HKL-3000		data reduction
HKL-3000		data scaling

Refinement

Method to determine structure:

SAD / Resolution: 1.9→102.06 Å / Cor.coef. F_o:F_c: 0.962 / Cor.coef. F_o:F_c free: 0.946 / SU B: 5.884 / SU ML: 0.091 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R Free: 0.134 / Stereochemistry target values: MAXIMUM LIKELIHOOD

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.21858	3376	5.1 %	RANDOM
R_work	0.179	-	-	-
all	0.179	66838	-	-
obs	0.18145	66670	99.75 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK

Displacement parameters

B_iso mean: 14.582 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.47 Å²	0 Å²	0 Å²
2-	-	-0.47 Å²	0 Å²
3-	-	-	0.94 Å²

Refinement step

Cycle: LAST / Resolution: 1.9→102.06 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	5873	0	51	384	6308

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.024	0.022	6059
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.02	4140
X-RAY DIFFRACTION	r_angle_refined_deg	1.824	1.964	8148
X-RAY DIFFRACTION	r_angle_other_deg	0.988	3	10126
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.781	5	739
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	34.998	25	280
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	14.395	15	1121
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	12.702	15	21
X-RAY DIFFRACTION	r_chiral_restr	0.122	0.2	886
X-RAY DIFFRACTION	r_gen_planes_refined	0.008	0.02	6662
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	1210
X-RAY DIFFRACTION	r_mcbond_it	1.132	1.5	3656
X-RAY DIFFRACTION	r_mcbond_other	0.418	1.5	1520
X-RAY DIFFRACTION	r_mcangle_it	1.886	2	5856
X-RAY DIFFRACTION	r_scbond_it	3.091	3	2403
X-RAY DIFFRACTION	r_scangle_it	4.498	4.5	2290

Refine LS restraints NCS

Dom-ID: 2 / Auth asym-ID: A / Ens-ID: 2 / Number: 19 / Refine-ID: X-RAY DIFFRACTION

Type	Rms dev position (Å)	Weight position
medium positional	0.47	0.5
medium thermal	0.99	2

LS refinement shell

Resolution: 1.9→1.95 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.341	242	-
R_work	0.263	4519	-
obs	-	-	98.21 %

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	2.0651	0.5334	-0.1586	1.3875	-0.384	4.8902	0.0498	0.098	0.0803	-0.0947	0.0462	-0.1372	-0.2831	0.508	-0.096	0.1074	-0.038	0.006	0.2612	0.0113	0.0358	80.588	43.568	18.989
2	2.2107	0.0823	-0.6689	0.2731	0.7264	3.9615	0.1964	-0.4828	0.16	-0.0824	-0.1354	-0.0654	-0.4903	-0.0834	-0.061	0.193	-0.0265	-0.012	0.29	0.0044	0.0583	65.43	39.447	33.09
3	2.7563	-0.343	0.0919	1.8643	0.3503	2.4387	0.0698	-0.2689	0.2189	-0.0029	-0.0284	-0.3907	-0.1525	0.4752	-0.0414	0.1259	-0.0651	0.0001	0.2784	0.061	0.1199	70.741	29.334	26.136
4	2.2126	0.252	0.0729	1.1285	0.2647	1.3	0.0582	-0.1778	-0.3177	0.1002	-0.0871	0.1172	0.1105	-0.1356	0.0288	0.0708	-0.0442	-0.0112	0.1818	0.0477	0.0759	51.841	22.559	23.703
5	1.1831	0.5166	-0.318	1.0839	-0.1654	1.0703	0.0997	-0.2258	0.0976	0.1675	-0.1004	0.1728	-0.0736	-0.2092	0.0007	0.0984	0.0117	-0.001	0.2645	-0.0375	0.0389	50.823	37.627	32.756
6	1.2607	-0.5261	0.4969	2.4871	-0.5922	1.679	0.0233	0.0015	0.1283	0.0531	-0.0697	-0.138	-0.0283	0.1092	0.0464	0.0575	0.0149	-0.0255	0.0973	0.006	0.0308	75.156	49.251	5.793
7	1.1598	0.0554	0.4024	1.7666	-0.2943	1.4809	-0.0399	-0.0372	0.2243	-0.0194	-0.0131	0.072	-0.1943	-0.0451	0.053	0.0792	0.0299	-0.0229	0.0761	0.0043	0.0568	68.672	55.151	5.455
8	0.8187	-0.1991	0.094	1.2286	-0.2252	0.542	0.0114	0.0448	0.2214	0.0034	-0.0658	-0.217	-0.0138	0.1012	0.0543	0.0643	-0.0055	-0.0086	0.1199	0.0307	0.1172	75.326	53.162	0.6
9	0.5802	0.0961	0.1861	1.4521	1.2023	1.3447	0.0152	-0.019	0.0312	-0.201	-0.1691	0.027	-0.1197	-0.0528	0.1539	0.0842	0.0255	-0.0156	0.1177	0.0173	0.0717	73.992	42.694	8.909
10	1.2787	-0.5027	1.0881	1.4961	0.9367	2.4032	-0.0011	0.0422	0.0416	0.0558	0.0638	-0.0869	0.0725	0.1633	-0.0628	0.0122	0.0067	-0.0243	0.0898	0.0252	0.0852	83.848	38.098	16.462
11	1.9532	0.43	0.3136	3.9542	1.1689	0.456	0.1323	-0.0565	-0.1898	-0.0935	-0.1396	-0.0833	0.0577	0.0382	0.0072	0.0752	0.0665	0.0149	0.093	0.0356	0.081	77.698	25.775	1.989
12	1.0151	0.8025	-0.2836	0.9124	-0.7484	1.103	0.0815	0.0233	-0.059	-0.0723	0.0135	0.0047	0.2581	0.0769	-0.095	0.31	-0.021	-0.0012	0.1784	-0.0174	0.1608	62.311	16.972	-6.197
13	1.1906	-0.323	-0.1308	1.9083	-0.0772	5.3053	0.0403	0.2605	-0.2616	-0.467	-0.0889	0.1193	0.3087	-0.6826	0.0485	0.2563	0.0106	0.0019	0.2809	-0.0805	0.0831	69.582	26.121	-21.803
14	1.5275	0.2469	0.1769	2.0737	-0.304	2.1408	0.0047	0.0324	-0.3607	-0.1533	-0.0142	0.0109	0.4812	-0.1064	0.0094	0.2022	0.0119	0.0441	0.1137	0.0064	0.1045	77.521	24.316	-11.007
15	2.1912	0.6075	-0.2489	2.0666	0.0845	1.7297	-0.0538	0.039	-0.1887	0.0348	-0.0504	-0.316	0.1195	0.1087	0.1042	0.1103	0.0245	0.0327	0.0819	0.0306	0.0696	86.322	40.845	-12.437
16	5.1827	3.6535	-2.0339	3.2923	-1.4149	2.1279	0.6608	-0.3268	0.5926	0.4117	-0.4499	0.6062	-0.4611	-0.1216	-0.211	0.4018	-0.0001	0.1068	0.2426	-0.0501	0.1529	73.168	53.424	-13.984
17	1.4666	0.5633	-0.3342	0.7048	-0.1404	1.1667	-0.0699	0.3229	0.0466	-0.2104	0.0958	0.0396	-0.0356	-0.0619	-0.0258	0.1974	0.0248	-0.0279	0.1544	-0.004	0.0101	71.857	40.445	-25.243
18	2.8732	-0.3152	-0.0684	0.6092	-0.1134	0.8221	-0.0602	-0.0726	-0.2139	-0.1379	-0.0015	0.1072	0.0439	0.0337	0.0617	0.0513	0.0041	-0.0152	0.0364	-0.0011	0.0491	50.799	24.37	4.229
19	2.9452	0.4172	0.1805	1.2287	0.1037	0.2981	-0.0374	0.2229	0.2109	-0.1072	-0.0527	0.1421	0.0682	-0.0256	0.0901	0.0864	0.0006	-0.0339	0.0737	0.0059	0.0746	48.5	32.352	-1.121
20	1.1111	0.2148	0.4833	1.1019	0.1532	2.0467	-0.0142	-0.1471	-0.1341	-0.0449	-0.0653	0.2558	0.0785	-0.5421	0.0795	0.0713	-0.0128	-0.02	0.1898	-0.0212	0.1036	49.451	24.912	2.732
21	1.3599	-0.4505	2.9311	0.1834	-0.1887	26.7403	0.4759	-0.1659	-0.2954	0.014	-0.0088	0.094	4.9752	-1.9323	-0.4671	1.0059	-0.3958	-0.1098	0.2156	0.0542	0.104	67.642	19.796	4.654

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	41 - 56
2	X-RAY DIFFRACTION	2	A	57 - 78
3	X-RAY DIFFRACTION	3	A	79 - 114
4	X-RAY DIFFRACTION	4	A	115 - 187
5	X-RAY DIFFRACTION	5	A	188 - 269
6	X-RAY DIFFRACTION	6	A	270 - 302
7	X-RAY DIFFRACTION	7	A	303 - 342
8	X-RAY DIFFRACTION	8	A	343 - 365
9	X-RAY DIFFRACTION	9	A	366 - 382
10	X-RAY DIFFRACTION	10	A	389 - 409
11	X-RAY DIFFRACTION	11	A	410 - 418
12	X-RAY DIFFRACTION	12	B	43 - 55
13	X-RAY DIFFRACTION	13	B	56 - 78
14	X-RAY DIFFRACTION	14	B	79 - 114
15	X-RAY DIFFRACTION	15	B	115 - 162
16	X-RAY DIFFRACTION	16	B	163 - 187
17	X-RAY DIFFRACTION	17	B	188 - 272
18	X-RAY DIFFRACTION	18	B	273 - 301
19	X-RAY DIFFRACTION	19	B	302 - 337
20	X-RAY DIFFRACTION	20	B	338 - 381
21	X-RAY DIFFRACTION	21	B	382

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