PDB-9jth: Crystal structure of NahX from Pseudomonas sp. MC1

ID or keywords:

Entry

Database: PDB / ID: 9jth

Title

Crystal structure of NahX from Pseudomonas sp. MC1

Components

NahX

Keywords

UNKNOWN FUNCTION / naphthalene degradation metabolism / Iron binding protein / Heme binding protein

Function / homology

: / Corrinoid adenosyltransferase PduO/GlcC-like / Corrinoid adenosyltransferase PduO/GlcC-like superfamily / Haem degrading protein HbpS-like / NahX

Function and homology information

Biological species

Pseudomonas sp. MC1 (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.7 Å

Authors

Son, J. / Park, A.K. / Kim, H.W.

Funding support

Korea, Republic Of, 1items

Citation

Journal: To Be Published
Title: Crystal structure of NahX from Pseudomonas sp. MC1
Authors: Son, J. / Park, A.K. / Kim, H.W.

History

Deposition	Oct 4, 2024	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Oct 8, 2025	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	9jth.cif.gz	222.4 KB	Display	PDBx/mmCIF format
PDB format	pdb9jth.ent.gz	181.6 KB	Display	PDB format
PDBx/mmJSON format	9jth.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	9jth_validation.pdf.gz	447.4 KB	Display	wwPDB validaton report
Full document	9jth_full_validation.pdf.gz	453 KB	Display
Data in XML	9jth_validation.xml.gz	29.1 KB	Display
Data in CIF	9jth_validation.cif.gz	39.5 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/jt/9jth ftp://data.pdbj.org/pub/pdb/validation_reports/jt/9jth	HTTPS FTP

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Related structure data

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: NahX

B: NahX

C: NahX

D: NahX

59 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: NahX

B: NahX

C: NahX

D: NahX

A: NahX

B: NahX

C: NahX

D: NahX

defined by author&software
118 kDa, 8 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	108.169, 108.169, 198.058
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	98
Space group name H-M	I4₁22

Components on special symmetry positions

ID	Model	Components
1	1	A-299- HOH
2	1	B-256- HOH

#1: Protein	NahX Mass: 14739.866 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas sp. MC1 (bacteria) / Gene: nahX, pYIC1_54 / Production host: Escherichia coli (E. coli) / References: UniProt: G9G7K4
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 385 / Source method: isolated from a natural source / Formula: H₂O
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: 2.44 Å³/Da / Density % sol: 49.55 %
Crystal grow	Temperature: 296 K / Method: vapor diffusion Details: 0.1 M Sodium acetate pH 4.6, 0.02 M Calcium chloride, and 20 % (v/v) (+/-)-2-Methyl-2,4-pentanediol (MPD)

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Data collection

Diffraction

Mean temperature: 80 K / Serial crystal experiment: N

Diffraction source

Source:

SYNCHROTRON / Site: PAL/PLS

/ Beamline: 5C (4A) / Wavelength: 0.97942 Å

Detector

Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Apr 14, 2021

Radiation

Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 0.97942 Å / Relative weight: 1

Reflection

Resolution: 1.7→50 Å / Num. obs: 64024 / % possible obs: 98.9 % / Redundancy: 18 % / CC_1/2: 1 / CC star: 1 / R_merge(I) obs: 0.075 / R_pim(I) all: 0.017 / R_rim(I) all: 0.077 / Χ²: 0.73 / Net I/σ(I): 6.3

Reflection shell

Diffraction-ID: 1

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Num. unique obs	CC_1/2	CC star	R_pim(I) all	R_rim(I) all	Χ²	% possible all
1.7-1.73	11.1	0.475	2464	0.622	0.876	0.14	0.496	0.32	77.7
1.73-1.76	12.9	0.443	3209	0.803	0.944	0.121	0.46	0.338	99.8
1.76-1.79	13.3	0.423	3182	0.812	0.947	0.114	0.439	0.351	100
1.79-1.83	13.5	0.397	3204	0.89	0.97	0.106	0.411	0.363	100
1.83-1.87	14.2	0.365	3213	0.926	0.981	0.095	0.377	0.404	100
1.87-1.91	14.2	0.342	3167	0.946	0.986	0.089	0.354	0.457	100
1.91-1.96	14.1	0.309	3223	0.956	0.989	0.081	0.32	0.579	99.9
1.96-2.02	16.2	0.257	3219	0.977	0.994	0.062	0.265	0.51	99.9
2.02-2.07	17.6	0.239	3180	0.983	0.996	0.056	0.246	0.628	100
2.07-2.14	18.2	0.209	3213	0.989	0.997	0.048	0.214	0.659	100
2.14-2.22	18.9	0.171	3221	0.993	0.998	0.039	0.176	0.719	100
2.22-2.31	18.5	0.169	3225	0.994	0.999	0.039	0.173	0.795	99.9
2.31-2.41	17.9	0.134	3233	0.996	0.999	0.031	0.137	0.768	100
2.41-2.54	21.2	0.117	3213	0.997	0.999	0.025	0.12	0.793	100
2.54-2.7	21.5	0.101	3239	0.998	1	0.021	0.103	0.81	100
2.7-2.91	21.9	0.085	3269	0.999	1	0.018	0.087	0.857	99.9
2.91-3.2	21.1	0.067	3252	0.999	1	0.014	0.069	0.929	99.9
3.2-3.66	24.5	0.053	3293	1	1	0.011	0.054	1.012	100
3.66-4.61	22.9	0.044	3315	1	1	0.009	0.045	1.032	99.9
4.61-50	23.8	0.046	3490	1	1	0.009	0.047	1.071	99.9

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Processing

Software

Name	Version	Classification
PHENIX	(1.20.1_4487: ???)	refinement
HKL-2000		data scaling
HKL-2000		data reduction
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.7→49.51 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.46 / Phase error: 19.73 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2083	1999	3.12 %
R_work	0.1985	-	-
obs	0.1989	64006	99.76 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL

Refinement step

Cycle: LAST / Resolution: 1.7→49.51 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4088	0	0	385	4473

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.008
X-RAY DIFFRACTION	f_angle_d	1.111
X-RAY DIFFRACTION	f_dihedral_angle_d	14.088	1470
X-RAY DIFFRACTION	f_chiral_restr	0.064	646
X-RAY DIFFRACTION	f_plane_restr	0.027	740

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 (%)
1.7-1.75	0.3037	137	0.3007	4252	X-RAY DIFFRACTION	97
1.75-1.79	0.274	141	0.2742	4369	X-RAY DIFFRACTION	100
1.79-1.85	0.2738	141	0.2504	4386	X-RAY DIFFRACTION	100
1.85-1.91	0.2669	141	0.2414	4371	X-RAY DIFFRACTION	100
1.91-1.97	0.2442	142	0.2235	4389	X-RAY DIFFRACTION	100
1.97-2.05	0.2133	143	0.2161	4409	X-RAY DIFFRACTION	100
2.05-2.15	0.2085	141	0.2116	4390	X-RAY DIFFRACTION	100
2.15-2.26	0.2187	142	0.2022	4409	X-RAY DIFFRACTION	100
2.26-2.4	0.2293	143	0.2012	4442	X-RAY DIFFRACTION	100
2.4-2.59	0.199	142	0.1974	4413	X-RAY DIFFRACTION	100
2.59-2.85	0.2174	145	0.202	4476	X-RAY DIFFRACTION	100
2.85-3.26	0.2089	144	0.1891	4455	X-RAY DIFFRACTION	100
3.26-4.11	0.169	145	0.1638	4522	X-RAY DIFFRACTION	100
4.11-49.51	0.1914	152	0.1848	4724	X-RAY DIFFRACTION	100

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	6.2169	-4.409	6.7459	7.7956	-6.5134	8.8034	0.1234	-0.7064	-0.1343	-0.1702	0.3936	0.8737	-0.1856	-0.8362	-0.5229	0.2599	0.0346	0.0893	0.2351	-0.0441	0.3021	29.9547	7.0756	23.645
2	2.5278	-1.271	-0.0782	3.1615	-0.0386	1.3252	0.0527	-0.1778	-0.1432	0.3877	-0.055	0.0854	0.1415	-0.0383	0.0116	0.2322	-0.0376	-0.0007	0.0927	0.0048	0.1169	52.4031	-6.1107	28.8164
3	4.0038	-0.8726	1.6902	0.3714	-0.1701	2.5244	0.1193	0.1318	-0.4367	-0.1209	-0.0018	0.1636	0.2733	-0.117	-0.0755	0.2391	-0.0085	0.0011	0.0841	-0.0184	0.2068	43.3187	-14.5245	13.7092
4	2.3234	-1.9857	-0.3887	7.0182	1.2921	4.5869	-0.1687	-0.0373	-0.5508	0.6005	-0.129	0.9963	0.1256	-0.6471	0.3313	0.2286	-0.0509	0.0975	0.1324	-0.0099	0.2206	40.342	-9.3693	26.5679
5	3.1224	-2.4611	1.0204	8.883	1.5655	1.1477	-0.1962	-0.3343	-0.6333	0.5964	0.1702	1.0018	0.5791	-0.3459	0.0846	0.3437	-0.0623	0.0145	0.2097	0.0972	0.282	46.948	-14.4065	31.1102
6	6.5049	-4.0022	-6.1506	5.1378	5.0325	8.7936	-0.3928	-0.6258	-0.3033	0.6759	0.0635	0.0905	0.7783	0.4577	0.3031	0.2726	0.0033	-0.1013	0.2042	0.0352	0.208	73.8552	-5.2171	28.0001
7	0.4789	0.3331	0.3595	1.4207	1.1137	2.2701	0.0595	0.238	-0.0108	-0.1833	-0.1187	-0.3469	-0.0175	0.3513	0.0664	0.1979	0.1079	-0.0027	0.2629	0.0417	0.2406	79.4641	-14.8074	2.7689
8	1.9539	0.0154	-0.9217	1.4978	2.0473	3.2693	0.0793	0.0291	-0.0854	-0.0079	0.0249	-0.0853	0.2689	0.4054	-0.1213	0.163	0.0749	-0.0092	0.1367	0.0153	0.1561	73.2164	-9.9346	3.1714
9	0.3177	0.2622	-1.1964	0.6547	0.3552	7.0652	0.072	0.1241	0.0582	-0.0167	-0.0684	0.1542	-0.5002	-0.3479	0.0369	0.1658	0.073	-0.018	0.1349	-0.0086	0.1845	65.4384	-13.3563	5.4619
10	2.1696	1.1792	-0.4619	2.5095	0.8198	1.9922	0.0785	-0.1828	-0.9835	0.0568	-0.0434	-0.3183	0.6225	0.2553	-0.0195	0.2597	0.063	-0.0221	0.1511	0.023	0.265	61.8476	-24.8372	13.1271
11	4.3384	-1.191	-2.943	1.3637	-0.2936	3.6661	0.055	0.3323	-0.1812	-0.0928	0.0624	0.2672	0.2703	-0.1664	-0.1561	0.2196	0.0324	-0.0627	0.1438	-0.0268	0.1945	54.4337	-20.4256	10.2375
12	6.1837	0.7394	1.6539	6.9939	0.5866	3.5662	0.3266	-0.7832	-0.6013	1.2413	-0.1351	-0.6858	0.785	0.0584	-0.1588	0.3982	0.0469	-0.0996	0.2127	0.0755	0.3351	74.9272	-19.946	18.4
13	3.1594	-0.232	-1.0047	5.7184	3.2736	4.092	0.1237	0.0147	-0.1752	0.2194	-0.137	-0.1188	0.2552	0.0738	-0.0131	0.1581	0.0679	-0.0155	0.1217	0.0087	0.2022	72.1194	-17.3381	9.4953
14	2.7021	-1.6778	-2.596	4.7199	2.176	3.4053	-0.0545	-0.1244	-0.5493	0.3496	0.0323	-0.0407	0.3357	0.1484	0.0931	0.2724	0.1412	0.0462	0.2192	0.046	0.2778	76.7992	-22.7809	6.1835
15	8.9956	1.073	-8.976	0.3409	-1.0355	9.5864	-0.0843	0.9418	0.056	-0.3834	-0.1485	-0.0536	0.2613	-0.3794	0.2239	0.3787	0.1704	-0.0634	0.4443	-0.0033	0.2647	32.6439	5.119	-19.3427
16	3.1972	2.0035	-1.7914	4.5022	-4.4135	8.3943	0.0219	0.0853	-0.0827	-0.0019	0.1445	0.6812	-0.1895	-1.1281	-0.1757	0.1697	0.0592	-0.0396	0.3671	-0.0799	0.3543	22.0164	1.7916	2.0706
17	4.9389	0.8591	-2.6163	4.1801	-2.6942	5.2463	0.3265	-0.1304	0.1038	0.0722	-0.1706	0.4458	-0.3716	-0.2776	-0.1463	0.1531	0.0282	-0.0163	0.1814	-0.0812	0.2449	29.2352	-2.029	4.7355
18	3.7025	0.6802	-1.7589	4.1716	-1.4498	4.9838	0.3184	0.5287	-0.1103	-0.3684	-0.0875	0.0696	-0.128	-0.3097	-0.2658	0.1791	0.0771	-0.0023	0.1736	-0.0227	0.2283	33.7424	3.157	-2.8751
19	1.0249	-0.7014	-0.0387	0.5503	0.1959	4.2288	0.0362	-0.0579	-0.1559	0.1894	0.0232	0.0495	0.2495	-0.1576	-0.0521	0.1817	-0.0039	0.0187	0.1413	-0.0279	0.218	30.4652	-2.2493	13.8871
20	1.9671	-1.3336	-0.7031	2.2107	-0.0507	3.694	0.1788	0.3324	-0.4049	-0.191	-0.0831	0.1568	0.3317	-0.1152	-0.1026	0.1776	0.0383	-0.0618	0.1706	-0.0602	0.2484	36.1497	-10.3985	-2.8055
21	9.653	-1.8072	-2.0641	6.2727	2.7299	5.9375	-0.1015	0.213	-1.2034	-0.3574	0.1463	0.4886	0.8904	-0.0835	-0.0139	0.4166	0.057	-0.1234	0.2732	-0.0967	0.3829	45.119	-24.3358	-7.5827
22	4.134	-1.2384	-2.1239	1.8338	-0.4897	1.9697	0.1433	-0.1345	-0.0268	-0.0011	-0.1701	0.0741	0.2218	0.1326	0.0459	0.3211	0.0531	-0.098	0.2311	-0.095	0.2652	41.4874	-12.0274	-2.1139
23	7.017	0.8503	-2.9544	4.3611	0.6113	1.4651	0.3339	1.1215	-0.1223	-1.5264	0.1521	0.5564	0.8584	-0.9705	-0.3693	0.5185	0.0475	-0.2291	0.4351	-0.1523	0.4507	26.3433	-5.6631	-14.0689
24	2.1572	-0.9635	-0.4375	3.2193	-3.2551	6.9955	0.0881	0.2684	-0.1567	-0.3666	-0.2374	0.3883	0.4125	-0.2692	0.1154	0.2001	0.033	-0.0633	0.2037	-0.1067	0.2369	29.7342	-5.8711	-1.5892
25	3.7559	-2.0933	0.5152	7.1779	-3.5929	6.9218	0.1006	0.4734	-0.7977	-0.9385	0.2989	1.1194	0.7832	-0.7576	-0.44	0.2715	-0.0889	-0.0596	0.4473	-0.1443	0.4516	22.6782	-7.7783	-0.3773
26	0.4116	0.8948	-0.1375	2.1795	-0.0413	0.3704	0.3668	0.1118	-0.352	-0.348	-0.2867	-0.539	0.0738	0.2776	-0.0923	0.4113	0.2476	0.1043	0.6054	0.0048	0.2926	78.2023	-6.5603	-17.5464
27	1.5531	-0.1311	-0.4899	0.3128	-0.1669	0.3307	0.2369	0.8887	-0.0485	-0.7133	-0.1781	0.3192	0.0583	-0.1774	0.0417	0.5186	0.3884	0.0044	0.6779	-0.1807	0.0251	51.8936	-7.1441	-25.6211
28	2.4723	1.7818	0.7188	1.4208	0.1555	1.2239	0.1202	0.3099	-0.3489	-0.293	-0.1698	-0.072	0.0179	-0.0241	0.0585	0.3427	0.195	-0.0216	0.3543	-0.0361	0.1905	53.1142	-4.346	-18.2106
29	2.1172	-0.7089	0.0182	1.3019	0.5507	1.9756	0.1102	-0.0138	0.1031	-0.1279	-0.1179	0.0872	-0.0755	-0.0278	0.0069	0.3009	0.1558	-0.0516	0.3092	-0.0802	0.1837	53.9078	-10.2689	-11.7037
30	1.082	0.2841	-0.8735	0.074	-0.2896	3.2445	0.1713	0.3484	-0.4861	-0.193	-0.1105	0.0249	0.3942	-0.2053	0.0142	0.412	0.175	-0.1125	0.3482	-0.1654	0.3117	58.1388	-23.7883	-11.3397
31	7.0309	-4.7331	-3.1598	6.2349	2.3783	8.9957	0.0617	0.4935	-1.0089	-0.3172	-0.1742	0.5133	0.7745	-0.4123	0.097	0.2845	0.0418	-0.0407	0.2354	-0.0894	0.3216	57.1026	-27.6149	0.6278
32	3.2876	-0.9742	2.5297	1.9998	-2.6556	4.0697	0.0564	-0.1173	0.2135	-0.2736	-0.2278	0.5337	-0.4032	-0.4871	0.1743	0.2799	0.1046	-0.0215	0.2225	-0.0619	0.317	55.0617	-15.5728	-5.9467
33	3.5374	-1.801	1.3333	7.2087	-0.0007	1.9044	-0.4421	0.5611	-1.3502	-0.601	0.0116	-1.1326	0.5002	0.9367	0.3878	0.475	0.2634	0.0398	0.6688	-0.0912	0.4781	66.9114	-16.9423	-22.103
34	6.6351	0.6579	-2.6607	2.0825	0.5532	3.6688	-0.1643	0.2478	-0.6206	-0.3086	-0.2015	0.0429	0.2585	-0.0473	0.272	0.3797	0.2236	-0.0841	0.3759	-0.155	0.2148	55.0716	-12.8667	-19.0136
35	2.6653	0.4131	-0.5677	4.0129	1.1749	2.0107	-0.2318	0.0859	-0.7372	0.0899	0.0507	0.0406	0.841	0.0395	0.3393	0.6997	0.4094	-0.0978	0.624	-0.4629	0.3023	51.2044	-16.9067	-24.3372

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 1 through 11 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 12 through 54 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 55 through 103 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 104 through 123 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 124 through 139 )
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 1 through 11 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 12 through 39 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 40 through 54 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 55 through 71 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 72 through 82 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 83 through 103 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 104 through 111 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 112 through 123 )
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 124 through 139 )
15	X-RAY DIFFRACTION	15	chain 'C' and (resid 3 through 11 )
16	X-RAY DIFFRACTION	16	chain 'C' and (resid 12 through 29 )
17	X-RAY DIFFRACTION	17	chain 'C' and (resid 30 through 39 )
18	X-RAY DIFFRACTION	18	chain 'C' and (resid 40 through 49 )
19	X-RAY DIFFRACTION	19	chain 'C' and (resid 50 through 54 )
20	X-RAY DIFFRACTION	20	chain 'C' and (resid 55 through 82 )
21	X-RAY DIFFRACTION	21	chain 'C' and (resid 83 through 91 )
22	X-RAY DIFFRACTION	22	chain 'C' and (resid 92 through 103 )
23	X-RAY DIFFRACTION	23	chain 'C' and (resid 104 through 112 )
24	X-RAY DIFFRACTION	24	chain 'C' and (resid 113 through 123 )
25	X-RAY DIFFRACTION	25	chain 'C' and (resid 124 through 139 )
26	X-RAY DIFFRACTION	26	chain 'D' and (resid 1 through 11 )
27	X-RAY DIFFRACTION	27	chain 'D' and (resid 12 through 39 )
28	X-RAY DIFFRACTION	28	chain 'D' and (resid 40 through 54 )
29	X-RAY DIFFRACTION	29	chain 'D' and (resid 55 through 71 )
30	X-RAY DIFFRACTION	30	chain 'D' and (resid 72 through 82 )
31	X-RAY DIFFRACTION	31	chain 'D' and (resid 83 through 91 )
32	X-RAY DIFFRACTION	32	chain 'D' and (resid 92 through 103 )
33	X-RAY DIFFRACTION	33	chain 'D' and (resid 104 through 112 )
34	X-RAY DIFFRACTION	34	chain 'D' and (resid 113 through 123 )
35	X-RAY DIFFRACTION	35	chain 'D' and (resid 124 through 137 )

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