PDB-3h02: 2.15 Angstrom Resolution Crystal Structure of Naphthoate Synthase...

ID or keywords:

Entry

Database: PDB / ID: 3h02

Title

2.15 Angstrom Resolution Crystal Structure of Naphthoate Synthase from Salmonella typhimurium.

Components

Naphthoate synthase

Keywords

LYASE / Naphthoate Synthase / idp00995 / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID

Function / homology

Function and homology information

1,4-dihydroxy-2-naphthoyl-CoA synthase / 1,4-dihydroxy-2-naphthoyl-CoA synthase activity / menaquinone biosynthetic process / cytosol
Similarity search - Function

Biological species

Salmonella typhimurium (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 2.15 Å

Authors

Minasov, G. / Wawrzak, Z. / Skarina, T. / Onopriyenko, O. / Peterson, S.N. / Savchenko, A. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID) / Center for Structural Genomics of Infectious Diseases (CSGID)

Citation

Journal: TO BE PUBLISHED
Title: 2.15 Angstrom Resolution Crystal Structure of Naphthoate Synthase from Salmonella typhimurium.
Authors: Minasov, G. / Wawrzak, Z. / Skarina, T. / Onopriyenko, O. / Peterson, S.N. / Savchenko, A. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)

History

Deposition	Apr 8, 2009	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Apr 21, 2009	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Advisory / Version format compliance
Revision 1.2	Nov 1, 2017	Group: Refinement description / Category: software / Item: _software.name

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	3h02.cif.gz	322.2 KB	Display	PDBx/mmCIF format
PDB format	pdb3h02.ent.gz	278.4 KB	Display	PDB format
PDBx/mmJSON format	3h02.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	3h02_validation.pdf.gz	500.2 KB	Display	wwPDB validaton report
Full document	3h02_full_validation.pdf.gz	522.5 KB	Display
Data in XML	3h02_validation.xml.gz	61.8 KB	Display
Data in CIF	3h02_validation.cif.gz	86.2 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/h0/3h02 ftp://data.pdbj.org/pub/pdb/validation_reports/h0/3h02	HTTPS FTP

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Related structure data

Similar structure data	4elx-d 4elw-d 4els-d 3t89-d 4jyl-d 6ojm-2 6ojm-3 5ir2-1 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
Other databases	TargetDB: idp00995

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#244 - Apr 2020 Photosynthetic Supercomplexes similarity (1) #49 - Jan 2004 Carbonic Anhydrase similarity (1) #59 - Nov 2004 Photosystem II similarity (1)

Deposited unit

A: Naphthoate synthase

B: Naphthoate synthase

C: Naphthoate synthase

D: Naphthoate synthase

E: Naphthoate synthase

F: Naphthoate synthase

hetero molecules

196 kDa, 6 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author&software

2

A: Naphthoate synthase

B: Naphthoate synthase

C: Naphthoate synthase

hetero molecules

defined by software
98 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

3

D: Naphthoate synthase

E: Naphthoate synthase

F: Naphthoate synthase

hetero molecules

defined by software
98 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	75.897, 132.819, 151.791
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Protein	Naphthoate synthase / Dihydroxynaphtoic acid synthetase Mass: 32564.041 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Salmonella typhimurium (bacteria) / Strain: LT2 / Gene: menB, STM2307 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-DE3 References: UniProt: Q7CQ56, 1,4-dihydroxy-2-naphthoyl-CoA synthase
#2: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO₄
#3: Chemical	ChemComp-BCT / BICARBONATE ION Mass: 61.017 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: CHO₃ / Comment: pH buffer*YM
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 626 / 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: 1.96 Å³/Da / Density % sol: 37.18 %
Crystal grow	Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: Protein solution: 0.3M NaCl, 10mM HEPES (pH 7.5); Screen solution: 20% PEG-3350, 0.2M Sodium Sulphate,0.1M B-Tris (pH 5.5); Freezing: Paratone, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 0.97925 Å
Detector	Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Feb 8, 2009 / Details: mirrors
Radiation	Monochromator: Si {1,1,1} / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97925 Å / Relative weight: 1
Reflection	Resolution: 2.15→30 Å / Num. all: 82913 / Num. obs: 82913 / % possible obs: 98.9 % / Observed criterion σ(I): -3 / Redundancy: 14.9 % / B_iso Wilson estimate: 29.6 Å² / R_merge(I) obs: 0.088 / Net I/σ(I): 43.5
Reflection shell	Resolution: 2.15→2.19 Å / Redundancy: 14.6 % / R_merge(I) obs: 0.487 / Mean I/σ(I) obs: 6.1 / Num. unique all: 4069 / % possible all: 98.2

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Processing

Software

Name	Version	Classification
Blu-Ice	Max	data collection
SHARP		phasing
REFMAC	5.5.0051	refinement
HKL-2000		data reduction
HKL-2000		data scaling

Refinement

Method to determine structure:

SAD / Resolution: 2.15→29.83 Å / Cor.coef. F_o:F_c: 0.957 / Cor.coef. F_o:F_c free: 0.935 / SU B: 10.187 / SU ML: 0.122 / TLS residual ADP flag: LIKELY RESIDUAL
Isotropic thermal model: Individual Atomic Temperature Factors Refined
Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.26 / ESU R Free: 0.193 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2152	4153	5 %	RANDOM
R_work	0.16858	-	-	-
all	0.17096	78544	-	-
obs	0.17096	78544	98.62 %	-

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: 18.788 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.7 Å²	0 Å²	0 Å²
2-	-	-2.25 Å²	0 Å²
3-	-	-	1.54 Å²

Refinement step

Cycle: LAST / Resolution: 2.15→29.83 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	12084	0	38	626	12748

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.01	0.022	12600
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.02	8560
X-RAY DIFFRACTION	r_angle_refined_deg	1.356	1.952	17049
X-RAY DIFFRACTION	r_angle_other_deg	0.778	3	20804
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	2.777	5	1601
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	30.592	24.328	610
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	10.025	15	2161
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	13.652	15	96
X-RAY DIFFRACTION	r_chiral_restr	0.084	0.2	1823
X-RAY DIFFRACTION	r_gen_planes_refined	0.005	0.02	14407
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	2577
X-RAY DIFFRACTION	r_mcbond_it	1.05	1.5	7883
X-RAY DIFFRACTION	r_mcbond_other	0.303	1.5	3248
X-RAY DIFFRACTION	r_mcangle_it	1.765	2	12583
X-RAY DIFFRACTION	r_scbond_it	3.295	3	4717
X-RAY DIFFRACTION	r_scangle_it	4.869	4.5	4466

LS refinement shell

Resolution: 2.15→2.208 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.233	270	-
R_work	0.168	5543	-
obs	-	5543	95.51 %

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	2.9193	-0.6554	0.8573	2.504	-0.0677	2.3811	0.0621	0.1941	-0.0463	-0.2556	0.0254	-0.166	-0.0029	0.18	-0.0876	0.1256	-0.0498	0.0815	0.0741	-0.0396	0.0575	57.7066	-16.6645	29.1256
2	0.4453	-0.0524	0.0335	1.6471	0.6819	0.8018	-0.049	0.0974	0.055	-0.1907	0.02	-0.0884	-0.0437	0.0383	0.029	0.074	-0.0304	0.0556	0.056	0.0136	0.0869	56.1944	-3.9663	39.3492
3	2.2045	-0.0751	-0.7726	0.6274	0.1028	0.7003	-0.1566	-0.0319	-0.1355	-0.0117	0.0856	-0.0594	0.1404	0.082	0.071	0.0364	0.0025	0.0227	0.05	0.002	0.0302	53.7394	-16.5714	47.1785
4	10.102	3.2206	1.8648	4.6361	3.8832	5.0413	0.3528	0.3825	-0.6711	0.2943	-0.3542	0.1438	0.7695	-0.528	0.0013	0.2488	-0.0658	-0.0219	0.1174	0.0039	0.2888	23.9762	-32.3734	56.129
5	2.7308	0.3532	-0.0894	2.5647	0.2895	1.9762	-0.0747	-0.4812	-0.1702	0.388	-0.0783	-0.1395	0.2157	0.2373	0.1531	0.0877	0.0442	0.0051	0.1867	0.1116	0.0879	57.012	-19.8641	82.4573
6	2.5424	-0.4422	-0.2942	1.1492	0.0408	2.5769	-0.0238	-0.0362	-0.1356	-0.0665	-0.0566	0.0008	0.1448	0.0447	0.0805	0.0155	0.0029	-0.0032	0.0624	0.0547	0.0688	54.8146	-16.4779	70.5787
7	0.9289	-0.2399	0.132	0.9573	-0.0179	0.946	-0.0473	-0.1115	0.0158	0.0179	-0.0354	-0.1634	-0.0353	0.1942	0.0826	0.0073	-0.0084	0.0006	0.0871	0.0336	0.0659	57.9214	-7.1314	67.443
8	6.6189	-0.0838	-2.3224	1.9371	0.907	4.3127	0.0964	-0.6262	-0.0264	0.5664	0.0346	0.2184	-0.2888	-0.1988	-0.1309	0.3703	0.0107	0.0723	0.2904	-0.0547	0.1495	32.709	15.1073	86.2072
9	2.8463	0.2904	-0.769	2.3247	-0.5062	2.6713	0.034	-0.1423	0.2497	0.1724	-0.0252	-0.3341	-0.4708	0.1159	-0.0088	0.1712	-0.0816	-0.0307	0.0626	-0.0041	0.19	59.8567	26.2476	58.6792
10	0.3172	0.2893	-0.1991	2.0257	-1.0784	1.6462	-0.0417	-0.0656	0.0355	0.0331	-0.0635	-0.3559	-0.1306	0.1985	0.1052	0.0338	-0.0382	-0.0226	0.1066	0.0139	0.1259	60.7852	8.7447	64.5941
11	1.1205	0.424	-0.0946	0.5145	0.1252	1.4268	-0.0991	0.1054	0.1137	-0.1636	0.0595	-0.1654	-0.2072	0.0325	0.0396	0.0832	-0.0363	0.04	0.0507	0.026	0.1646	54.1055	14.8978	45.7401
12	3.753	-3.1339	0.3872	10.0154	-1.9518	4.4056	0.2232	0.4044	0.6826	-1.009	-0.1178	0.1532	-0.5344	-0.2001	-0.1053	0.6345	0.0152	-0.0988	0.4637	0.1551	0.4381	28.8189	18.2448	27.6477
13	3.1423	-0.3341	0.0365	2.9633	-0.5303	2.0856	-0.0781	0.5266	-0.1031	-0.5013	0.107	0.0939	0.2553	-0.0587	-0.0289	0.2637	-0.1018	-0.043	0.2229	-0.02	0.0147	21.281	-9.5925	29.2989
14	0.9978	0.2446	0.5155	0.5357	-0.5271	1.7154	-0.0473	0.095	-0.1135	-0.2052	0.0904	0.0377	0.1498	-0.1014	-0.0431	0.1079	-0.03	-0.0272	0.0748	-0.0037	0.058	22.7506	-10.6446	47.7594
15	1.8295	0.5945	-0.0044	0.9216	0.0332	0.3385	-0.1715	0.2214	0.1517	-0.2712	0.1233	0.0253	0.02	-0.065	0.0483	0.1018	-0.038	-0.0056	0.0956	0.0288	0.0306	26.2041	3.4844	38.8269
16	4.9345	-0.4725	-3.8057	2.2945	-0.8511	6.6271	0.2323	0.3853	0.1623	-0.3504	-0.1991	-0.112	-0.6258	0.1319	-0.0332	0.3414	-0.0114	0.0425	0.239	0.0921	0.193	54.5034	18.3408	29.9036
17	2.5828	-0.0878	0.0788	1.9999	-0.6173	2.6742	-0.0606	-0.0597	0.2549	0.1729	0.0994	0.0878	-0.4266	-0.0619	-0.0388	0.1327	0.0251	0.0494	0.0085	0.0059	0.077	26.3344	32.1272	60.7943
18	1.8239	-0.0969	0.0662	1.9527	0.4238	2.6002	0.0545	0.0762	0.038	-0.0673	0.064	0.0496	-0.0921	0.0363	-0.1185	0.0474	0.0097	0.0423	0.0162	0.0228	0.0599	27.8592	21.3423	55.293
19	0.3962	-0.1925	-0.0914	1.163	-0.1982	0.8577	0.0075	-0.0254	0.0549	0.0722	0.062	0.1488	-0.0422	-0.0904	-0.0695	0.0239	-0.0026	0.0305	0.0419	0.0126	0.0595	25.87	12.7291	61.0809
20	9.8088	3.3859	4.2855	2.0571	2.8779	5.5584	0.1853	0.3199	0.0636	0.4784	-0.0231	-0.122	-0.102	0.2697	-0.1623	0.7028	-0.1501	-0.1242	0.3117	-0.0562	0.1788	54.2035	10.9011	87.1181
21	2.5426	0.8549	0.0885	3.4593	0.4234	2.2968	0.0997	-0.2578	-0.1331	0.378	-0.0263	0.0322	0.0771	-0.115	-0.0734	0.0656	-0.032	0.004	0.1276	0.0703	0.0565	22.0672	-18.0374	80.3039
22	1.0768	0.3316	-0.2155	3.1939	0.2425	1.0246	0.0566	-0.1545	0.0755	0.2173	-0.0217	-0.0251	-0.149	-0.011	-0.0349	0.059	-0.0171	0.0126	0.1118	0.0367	0.0593	24.692	-4.7972	75.5279
23	0.721	0.7702	-0.3498	1.4716	-0.0432	1.2026	-0.0022	0.0014	0.0343	-0.0187	0.075	0.1661	-0.0469	-0.1369	-0.0727	0.0029	0.001	0.0006	0.0839	0.054	0.0507	20.8676	-5.9699	66.3969
24	1.9501	0.6387	2.9139	8.1398	2.2443	4.7129	0.0053	0.09	-0.3395	0.3675	0.4682	-0.1376	0.2361	0.1915	-0.4735	0.1596	-0.0058	0.0493	0.1418	0.007	0.1501	40.4523	-18.4298	59.6528

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	5 - 63
2	X-RAY DIFFRACTION	2	A	64 - 188
3	X-RAY DIFFRACTION	3	A	189 - 264
4	X-RAY DIFFRACTION	4	A	265 - 285
5	X-RAY DIFFRACTION	5	B	7 - 63
6	X-RAY DIFFRACTION	6	B	64 - 167
7	X-RAY DIFFRACTION	7	B	168 - 254
8	X-RAY DIFFRACTION	8	B	255 - 285
9	X-RAY DIFFRACTION	9	C	7 - 116
10	X-RAY DIFFRACTION	10	C	117 - 197
11	X-RAY DIFFRACTION	11	C	198 - 266
12	X-RAY DIFFRACTION	12	C	267 - 285
13	X-RAY DIFFRACTION	13	D	5 - 84
14	X-RAY DIFFRACTION	14	D	85 - 197
15	X-RAY DIFFRACTION	15	D	198 - 257
16	X-RAY DIFFRACTION	16	D	258 - 285
17	X-RAY DIFFRACTION	17	E	6 - 61
18	X-RAY DIFFRACTION	18	E	62 - 167
19	X-RAY DIFFRACTION	19	E	168 - 257
20	X-RAY DIFFRACTION	20	E	258 - 285
21	X-RAY DIFFRACTION	21	F	5 - 79
22	X-RAY DIFFRACTION	22	F	80 - 162
23	X-RAY DIFFRACTION	23	F	163 - 238
24	X-RAY DIFFRACTION	24	F	239 - 260

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