PDB-4ocg: Structure of the Shewanella loihica PV-4 NADH-dependent persulfid...

ID or keywords:

Entry

Database: PDB / ID: 4ocg

Title

Structure of the Shewanella loihica PV-4 NADH-dependent persulfide reductase F161A Mutant

Components

FAD-dependent pyridine nucleotide-disulphide oxidoreductase

Keywords

OXIDOREDUCTASE / NADP-Dependant Reductase

Function / homology

Function and homology information

flavin adenine dinucleotide binding / oxidoreductase activity
Similarity search - Function

Biological species

Shewanella loihica (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.75 Å

Authors

Lee, K.-H. / Sazinsky, M.H. / Crane, E.J.

Citation

Journal: Biochim.Biophys.Acta / Year: 2014
Title: Characterization of the mechanism of the NADH-dependent polysulfide reductase (Npsr) from Shewanella loihica PV-4: Formation of a productive NADH-enzyme complex and its role in the general ...
Authors: Lee, K.H. / Humbarger, S. / Bahnvadia, R. / Sazinsky, M.H. / Crane, E.J.

History

Deposition	Jan 9, 2014	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Aug 20, 2014	Provider: repository / Type: Initial release
Revision 1.1	Aug 23, 2017	Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.detector
Revision 1.2	Nov 22, 2017	Group: Refinement description / Category: software / Item: _software.name
Revision 1.3	Feb 28, 2024	Group: Data collection / Database references / Derived calculations Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	4ocg.cif.gz	430.6 KB	Display	PDBx/mmCIF format
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Validation report

Summary document	4ocg_validation.pdf.gz	1.4 MB	Display	wwPDB validaton report
Full document	4ocg_full_validation.pdf.gz	1.4 MB	Display
Data in XML	4ocg_validation.xml.gz	44 KB	Display
Data in CIF	4ocg_validation.cif.gz	60.9 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/oc/4ocg ftp://data.pdbj.org/pub/pdb/validation_reports/oc/4ocg	HTTPS FTP

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Related structure data

Similar structure data	3nta-d 3nt6-d 3ntd-d 4a0r-d 4yao-d 4a0g-1 6wwj-d 4c8s-d 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	#154 - Oct 2012 Citric Acid Cycle similarity (6) #153 - Sep 2012 Pyruvate Dehydrogenase Complex similarity (5) #82 - Oct 2006 Cytochrome p450 similarity (2) #146 - Feb 2012 Aminoglycoside Antibiotics similarity (1) #93 - Sep 2007 Citrate Synthase similarity (1) #216 - Dec 2017 Biodegradable Plastic similarity (1) #39 - Mar 2003 lac Repressor similarity (1)

Deposited unit

A: FAD-dependent pyridine nucleotide-disulphide oxidoreductase

B: FAD-dependent pyridine nucleotide-disulphide oxidoreductase

hetero molecules

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

1

Idetical with deposited unit
defined by author&software

2

A: FAD-dependent pyridine nucleotide-disulphide oxidoreductase

B: FAD-dependent pyridine nucleotide-disulphide oxidoreductase

hetero molecules

A: FAD-dependent pyridine nucleotide-disulphide oxidoreductase

B: FAD-dependent pyridine nucleotide-disulphide oxidoreductase

hetero molecules

A: FAD-dependent pyridine nucleotide-disulphide oxidoreductase

B: FAD-dependent pyridine nucleotide-disulphide oxidoreductase

hetero molecules

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

Unit cell

Length a, b, c (Å)	133.710, 133.710, 84.317
Angle α, β, γ (deg.)	90.00, 90.00, 120.00
Int Tables number	143
Space group name H-M	P3

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	A
2	1	B

NCS domain segments:

Dom-ID	Component-ID	Ens-ID	Refine code	Auth asym-ID	Auth seq-ID
1	1	1	4	A	1 - 600
2	1	1	4	B	1 - 600

#1: Protein	FAD-dependent pyridine nucleotide-disulphide oxidoreductase Mass: 62349.781 Da / Num. of mol.: 2 / Mutation: F161A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Shewanella loihica (bacteria) / Strain: PV-4 / Gene: Shew_0729 / Production host: Escherichia coli (E. coli) / References: UniProt: A3QAV3
#2: Chemical	ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE Mass: 785.550 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₂₇H₃₃N₉O₁₅P₂ / Comment: FAD*YM
#3: Chemical	ChemComp-COA / COENZYME A Mass: 767.534 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₂₁H₃₆N₇O₁₆P₃S
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 165 / 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: 3.49 Å³/Da / Density % sol: 64.75 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.7 Details: 200 mM ammonium acetate, 50 mM sodium citrate, 5% PEG 4000, pH 4.7, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

SSRL

/ Beamline: BL12-2 / Wavelength: 1 Å

Detector

Type: Pilatus / Detector: PIXEL / Date: Oct 1, 2010

Radiation

Monochromator: Liquid nitrogen-cooled double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 1 Å / Relative weight: 1

Reflection twin

Crystal-ID	ID	Operator	Domain-ID	Fraction
1	1	H, K, L	1	0.629
1	1	-H, H+K, -L	2	0.371

Reflection

Resolution: 2.75→50 Å / Num. all: 43765 / Num. obs: 42058 / % possible obs: 96.1 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 5.1 % / R_sym value: 0.06 / Net I/σ(I): 14.5

Reflection shell

Resolution: 2.75→2.81 Å / Mean I/σ(I) obs: 8.8 / R_sym value: 0.161 / % possible all: 88.5

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Processing

Software

Name	Version	Classification
Blu-Ice	Ice	data collection
MOLREP		phasing
REFMAC	5.5.0102	refinement
MOSFLM		data reduction
SCALA		data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.75→50 Å / Cor.coef. F_o:F_c: 0.965 / Cor.coef. F_o:F_c free: 0.93 / SU B: 23.116 / SU ML: 0.212 / Cross valid method: THROUGHOUT / ESU R: 0.104 / ESU R Free: 0.049 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.17307	2068	4.9 %	RANDOM
R_work	0.12233	-	-	-
obs	0.12483	40258	96.09 %	-
all	-	43765	-	-

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: 37.124 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-44.14 Å²	0 Å²	0 Å²
2-	-	-44.14 Å²	0 Å²
3-	-	-	88.29 Å²

Refinement step

Cycle: LAST / Resolution: 2.75→50 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	8583	0	202	165	8950

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.019	0.022	8942
X-RAY DIFFRACTION	r_bond_other_d
X-RAY DIFFRACTION	r_angle_refined_deg	2.002	1.993	12140
X-RAY DIFFRACTION	r_angle_other_deg
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	7.079	5	1128
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	37.713	24.444	396
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	19.91	15	1490
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	19.209	15	62
X-RAY DIFFRACTION	r_chiral_restr	0.125	0.2	1371
X-RAY DIFFRACTION	r_gen_planes_refined	0.008	0.021	6713
X-RAY DIFFRACTION	r_gen_planes_other
X-RAY DIFFRACTION	r_nbd_refined
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined
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
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined
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	0.683	1.5	5587
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it	1.317	2	8942
X-RAY DIFFRACTION	r_mcangle_other
X-RAY DIFFRACTION	r_scbond_it	2.298	3	3355
X-RAY DIFFRACTION	r_scbond_other
X-RAY DIFFRACTION	r_scangle_it	3.613	4.5	3198
X-RAY DIFFRACTION	r_scangle_other
X-RAY DIFFRACTION	r_long_range_B_refined
X-RAY DIFFRACTION	r_long_range_B_other
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 / Number: 4270 / Refine-ID: X-RAY DIFFRACTION

Type	Rms dev position (Å)	Weight position
medium positional	0.34	0.5
medium thermal	0.84	2

LS refinement shell

Resolution: 2.746→2.818 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.26	144	-
R_work	0.195	2650	-
obs	-	-	85.31 %

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	-0.115	-0.2079	-0.2042	0.9041	0.7943	0.9166	-0.0385	-0.0077	0.0274	0.0248	0.0524	-0.1327	0.142	-0.0014	-0.0138	0.0873	-0.0026	0.0053	0.0791	-0.0077	0.1742	54.8215	-12.5975	36.6165
2	0.5248	-0.2813	0.3944	0.2621	-0.2814	0.6026	0.0316	-0.042	0.0945	-0.0339	-0.0419	-0.0913	0.0535	-0.0492	0.0104	0.0776	-0.0025	0.0036	0.0692	-0.0042	0.1463	48.5104	-7.6601	34.8709
3	4.9063	-0.3226	0.5064	1.5695	-1.0876	0.5963	-0.0502	-0.25	-0.1352	0.1309	0.2211	0.1744	-0.0892	-0.1701	-0.1709	0.0629	0.011	0.0165	0.0708	-0.0136	0.1609	32.7405	-2.306	29.8908
4	0.1801	-0.1208	-0.1089	0.2698	0.0913	0.0704	0.0063	-0.0168	0.0556	-0.0222	0.0183	-0.1425	-0.0119	-0.0163	-0.0246	0.0623	-0.0184	0.0114	0.077	-0.0026	0.1591	52.803	-1.265	27.16
5	1.5186	-1.7802	0.0289	2.8004	-0.1225	-0.0161	0.0656	0.0275	-0.047	0.0591	-0.1041	0.1229	-0.0018	0.0222	0.0385	0.0867	-0.005	0.0315	0.0919	0.0153	0.1177	29.9785	-0.1311	12.6835
6	0.1418	0.243	-0.3785	3.0814	-0.1492	0.677	0.0144	0.0225	-0.0165	-0.2765	-0.0167	0.0181	-0.0502	-0.0133	0.0023	0.1121	-0.0137	-0.0086	0.0875	-0.0153	0.0705	30.2452	-14.2498	5.3187
7	0.2962	-0.6543	0.1381	2.23	-0.5676	0.0816	-0.0523	0.0599	-0.0141	-0.1894	0.0651	0.0938	0.0419	-0.0172	-0.0128	0.1269	-0.0468	0.0056	0.0755	0.0302	0.1172	32.6093	12.9052	4.2396
8	0.7419	0.4695	0.4064	1.4347	-0.7732	0.9078	-0.0369	0.053	0.0609	-0.1921	0.0285	0.0446	0.0951	0.0625	0.0083	0.0847	-0.0117	0.0474	0.0877	0.0223	0.1076	36.426	4.2544	4.6819
9	1.2389	0.0317	0.3162	0.8062	0.2038	1.3753	-0.06	0.0269	-0.1155	-0.1146	0.0383	-0.155	0.0372	0.1011	0.0216	0.031	-0.0141	0.0611	0.0717	-0.0097	0.1744	60.4235	-15.9909	21.818
10	6.9558	4.3758	12.324	-0.0994	7.3438	21.3344	0.2652	-0.142	-0.2154	0.0763	-0.0131	-0.1055	0.1936	-0.313	-0.2521	0.1728	0.036	0.0901	0.0226	-0.0535	0.3407	52.7834	-22.1265	18.7901
11	0.1785	0.3202	0.4823	0.6723	0.5143	1.2038	0.0159	0.0366	-0.0577	0.0012	0.0599	-0.1583	0.0245	0.0615	-0.0758	0.0624	0.0037	0.0283	0.0782	-0.0037	0.1558	49.3919	-23.654	26.2004
12	1.7649	-1.4747	-0.9927	3.4839	0.6198	0.9121	-0.037	0.0051	0.0469	-0.2028	0.0377	-0.1562	-0.0517	0.0451	-0.0007	0.0582	-0.0133	0.0049	0.0834	-0.0227	0.0747	36.6636	-25.7306	9.0611
13	0.6077	-0.1089	-0.1806	0.633	-0.0698	0.2178	-0.018	0.0543	-0.0271	-0.0423	0.0112	-0.0307	-0.0009	-0.0352	0.0069	0.0782	-0.0099	0.0009	0.0749	-0.0149	0.1173	27.5063	-33.5361	18.0603
14	0.611	0.221	0.2737	1.3567	0.0481	1.0277	0.0451	0.0946	0.0094	-0.1626	0.052	-0.1363	0.0192	0.0993	-0.0971	0.0781	0.0086	0.0523	0.0811	-0.0319	0.0728	25.3036	-39.0485	-2.1035
15	0.8403	1.3109	-1.1086	7.6979	-0.7324	2.3071	0.0057	0.079	0.0493	-0.331	-0.0591	0.2848	-0.0978	-0.1122	0.0534	0.0648	0.0162	-0.0278	0.0741	0.0005	0.054	11.6843	-38.1574	-5.1139
16	1.0876	1.138	0.3402	1.2643	0.1314	0.1427	-0.0384	0.046	0.0213	-0.0107	0.0506	0.0677	-0.0453	0.0079	-0.0122	0.1475	-0.0229	0.0298	0.1151	-0.0399	0.0795	20.8393	-40.643	-2.6829
17	1.1299	0.6929	-0.3769	0.2996	-0.2121	2.2244	0.0152	0.0584	-0.0885	-0.0043	0.0103	-0.061	-0.1109	-0.1217	-0.0255	0.0523	0.0173	0.0135	0.079	-0.0269	0.1719	14.1362	-54.51	12.9998
18	0.3396	-0.3272	-0.1925	1.7305	0.7096	0.3071	0.0868	-0.0189	-0.1056	-0.0008	-0.1168	0.0567	-0.0428	-0.0853	0.03	0.0741	0.007	-0.0025	0.1089	0.0178	0.1214	4.7781	-44.9494	21.3715
19	0.8372	-0.1021	0.0405	0.3171	0.319	0.9155	0.0085	0.1014	-0.017	-0.0389	0.0056	-0.0858	-0.09	-0.1124	-0.0141	0.0904	-0.0005	0.0032	0.074	-0.0148	0.0906	3.9736	-43.9263	14.078
20	0.1826	0.041	-0.0674	0.2455	0.1994	0.358	-0.0176	-0.0189	-0.0712	0.0231	0.0147	0.0623	0.0496	-0.0432	0.0029	0.0692	-0.0116	0.0084	0.0713	0.0096	0.1625	1.9184	-55.8041	27.9607
21	3.1399	-1.1117	-1.8265	1.3172	-0.0254	1.1823	0.0465	0.0848	-0.1174	-0.1702	-0.1116	0.0011	0.0238	-0.0643	0.0652	0.0837	0.0239	0.0007	0.0986	0.0565	0.1182	-8.4117	-32.4014	36.7393
22	3.0868	-1.1544	1.4629	1.1553	-0.3387	0.3833	0.0608	0.0962	0.0855	-0.0703	-0.0339	-0.0787	0.0325	0.0647	-0.0269	0.1167	-0.0111	0.0382	0.0771	0.0066	0.1232	5.673	-31.8428	39.0132
23	1.8395	1.085	-0.1227	0.5507	-0.0878	0.0878	0.0745	-0.2126	0.1001	0.0575	-0.0659	0.0243	-0.0066	-0.0656	-0.0087	0.097	0.0097	-0.0066	0.1276	-0.0168	0.1099	13.6014	-31.5258	45.5321
24	0.9927	0.4391	0.211	0.1881	0.1635	0.0545	0.0403	-0.2536	0.0996	0.0348	-0.0857	0.0835	-0.001	-0.0191	0.0454	0.0881	-0.013	0.0116	0.1014	0.0318	0.1371	-2.5683	-32.9873	48.7219
25	1.2739	0.0225	-0.5742	0.285	0.2326	0.3904	0.0273	-0.0629	0.0013	0.005	-0.0261	0.0376	-0.0091	0.0088	-0.0012	0.0711	-0.0034	0.0185	0.0985	0.0192	0.1105	-7.9029	-33.813	46.3511
26	1.5219	-0.1492	0.3074	0.9405	0.13	1.421	-0.0036	-0.0457	-0.1429	0.0904	0.011	-0.045	0.0401	0.0562	-0.0074	0.0648	-0.0086	-0.0018	0.0408	0.02	0.1464	16.6302	-60.3314	30.0748
27	0.72	1.3475	-1.0571	1.4508	-1.1516	0.8141	0.0379	-0.0171	0.1184	0.05	0.0429	0.1362	-0.0026	0.0294	-0.0808	0.0792	0.0226	-0.0595	0.082	0.0273	0.2477	27.104	-51.2787	35.1063
28	0.322	0.0144	0.1465	-0.0046	0.009	0.2244	0.0107	-0.001	-0.0478	0.0181	-0.0128	-0.0208	0.0376	-0.0347	0.0021	0.0811	-0.0108	0.0046	0.0736	0.0179	0.1499	22.7073	-44.39	29.1818
29	0.9345	-1.1846	-0.9711	10.3695	0.2557	0.8934	-0.1698	-0.0817	-0.0528	0.2234	0.1734	0.067	0.1164	0.0511	-0.0036	0.0871	-0.0015	-0.0224	0.0543	0.0699	0.1482	33.6621	-38.2323	47.1381
30	0.1243	0.0828	-0.1342	0.1575	-0.1013	0.2571	0.0005	-0.0316	0.0173	0.0072	0.0337	-0.0753	0.0075	-0.0214	-0.0342	0.0808	-0.0012	-0.0119	0.0824	0.0011	0.1357	35.2372	-27.6349	35.2989
31	2.9743	0.3028	0.2204	2.1474	0.1879	0.9027	0.0572	-0.4166	0.0043	0.309	0.0725	0.1428	-0.0641	-0.2478	-0.1296	0.0889	0.027	0.0322	0.1406	0.031	0.0381	33.9739	-20.3239	59.3639
32	0.957	0.7246	-0.0628	0.5531	0.0786	0.1899	0.0419	-0.0037	0.0493	0.0562	-0.041	0.0263	-0.0286	-0.0525	-0.0009	0.1255	0.0008	-0.0359	0.1082	0.0114	0.1113	41.3589	-18.4675	54.9947

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	1 - 20
2	X-RAY DIFFRACTION	2	A	21 - 47
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