PDB-4fcc: Glutamate dehydrogenase from E. coli

ID or keywords:

Entry

Database: PDB / ID: 4fcc

Title

Glutamate dehydrogenase from E. coli

Components

Glutamate dehydrogenase

Keywords

OXIDOREDUCTASE / protein complex / ROSSMANN FOLD / METABOLIC ROLE / NAD / NADP

Function / homology

Function and homology information

glutamate biosynthetic process / glutamate dehydrogenase (NADP+) activity / nucleotide binding / cytosol
Similarity search - Function

Biological species

Escherichia coli O157:H7 (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2 Å

Authors

Bilokapic, S. / Schwartz, T.U.

Citation

Journal: Proc.Natl.Acad.Sci.USA / Year: 2012
Title: Molecular basis for Nup37 and ELY5/ELYS recruitment to the nuclear pore complex.
Authors: Bilokapic, S. / Schwartz, T.U.

History

Deposition	May 24, 2012	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Sep 26, 2012	Provider: repository / Type: Initial release
Revision 1.1	Oct 3, 2012	Group: Structure summary
Revision 1.2	Jan 9, 2013	Group: Database references
Revision 1.3	Feb 28, 2024	Group: Data collection / Database references Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	4fcc.cif.gz	2 MB	Display	PDBx/mmCIF format
PDB format	pdb4fcc.ent.gz	1.7 MB	Display	PDB format
PDBx/mmJSON format	4fcc.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	4fcc_validation.pdf.gz	511.7 KB	Display	wwPDB validaton report
Full document	4fcc_full_validation.pdf.gz	562.6 KB	Display
Data in XML	4fcc_validation.xml.gz	212 KB	Display
Data in CIF	4fcc_validation.cif.gz	308.6 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/fc/4fcc ftp://data.pdbj.org/pub/pdb/validation_reports/fc/4fcc	HTTPS FTP

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Related structure data

Related structure data	4fhlC 4fhmC 4fhnC C: citing same article (ref.)
Similar structure data	3sbo-d 4bht-d 4fhn-3 3aog-2 2tmg-d 6yeh-d 1euz-d 2yfq-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

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Glutamate dehydrogenase

B: Glutamate dehydrogenase

C: Glutamate dehydrogenase

D: Glutamate dehydrogenase

E: Glutamate dehydrogenase

F: Glutamate dehydrogenase

G: Glutamate dehydrogenase

H: Glutamate dehydrogenase

I: Glutamate dehydrogenase

J: Glutamate dehydrogenase

K: Glutamate dehydrogenase

L: Glutamate dehydrogenase

586 kDa, 12 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Glutamate dehydrogenase

B: Glutamate dehydrogenase

C: Glutamate dehydrogenase

D: Glutamate dehydrogenase

E: Glutamate dehydrogenase

F: Glutamate dehydrogenase

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

2

G: Glutamate dehydrogenase

H: Glutamate dehydrogenase

I: Glutamate dehydrogenase

J: Glutamate dehydrogenase

K: Glutamate dehydrogenase

L: Glutamate dehydrogenase

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

Unit cell

Length a, b, c (Å)	105.218, 176.262, 150.250
Angle α, β, γ (deg.)	90.000, 89.940, 90.000
Int Tables number	4
Space group name H-M	P12₁1

Details

The biological unit is a hexamer. There are 2 biological units in the asymmetric unit (chains A, B, C, D, E & F and chains G, H, I, J, K & L)

#1: Protein	Glutamate dehydrogenase Mass: 48864.406 Da / Num. of mol.: 12 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli O157:H7 (bacteria) / Gene: gdhA, ECs2467, Z2793 / Plasmid: modified pETduet / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q8XDW9
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 3833 / 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: 2.38 Å³/Da / Density % sol: 48.27 %
Crystal grow	Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 0.1 M Bis-Tris/HCl pH 6.5, 0.2 NH4Ac, 19% PEG6000, VAPOR DIFFUSION, HANGING DROP, temperature 291.0K

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Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

APS

/ Beamline: 24-ID-C / Wavelength: 0.97918 Å

Detector

Type: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 17, 2010

Radiation

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

Radiation wavelength

Wavelength: 0.97918 Å / Relative weight: 1

Reflection

Resolution: 1.999→49.653 Å / Num. all: 365923 / Num. obs: 365923 / % possible obs: 99.2 % / Observed criterion σ(I): -3 / Redundancy: 3.7 % / R_sym value: 0.175 / Net I/σ(I): 5.1

Reflection shell

Diffraction-ID: 1

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Mean I/σ(I) obs	Num. measured all	Num. unique all	R_sym value	% possible all
2-2.07	3.2	0.59	1.2	107166	33536	0.59	92.6
2.07-2.15	3.7	0.473	1.5	128348	34845	0.473	100
2.15-2.23	3.7	0.355	2.1	124251	33640	0.355	100
2.23-2.33	3.7	0.298	2.4	118970	32160	0.298	99.9
2.33-2.45	3.7	0.255	2.8	114447	30836	0.255	100
2.45-2.58	3.7	0.221	3.1	108464	29214	0.221	99.9
2.58-2.74	3.7	0.203	3.4	103362	27805	0.203	100
2.74-2.93	3.7	0.178	3.8	96865	26023	0.178	100
2.93-3.16	3.7	0.168	3.9	90359	24295	0.168	100
3.16-3.46	3.7	0.157	4	82818	22325	0.157	99.9
3.46-3.87	3.7	0.147	4.4	74644	20210	0.147	99.9
3.87-4.47	3.7	0.141	4.6	65532	17842	0.141	99.8
4.47-5.47	3.6	0.141	4.4	53996	15007	0.141	99.5
5.47-7.74	3.7	0.132	4.8	43198	11709	0.132	99.7
7.74-49.653	3.7	0.125	4.7	23876	6476	0.125	98.9

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Processing

Software

Name	Version	Classification
SCALA	3.3.20	data scaling
PHENIX	1.7.3_928	refinement
PDB_EXTRACT	3.11	data extraction
HKL-2000		data collection
DENZO		data reduction
ARP/wARP		model building

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2→49.653 Å / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.8518 / SU ML: 0.26 / σ(F): 1.35 / Phase error: 22.69 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.229	3646	1 %	RANDOM
R_work	0.1813	-	-	-
obs	0.1818	364127	98.98 %	-

Solvent computation

Shrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / B_sol: 65.022 Å² / k_sol: 0.4 e/Å³

Displacement parameters

B_iso max: 144.44 Å² / B_iso mean: 33.8518 Å² / B_iso min: 9.11 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-2.9551 Å²	0 Å²	-0.3374 Å²
2-	-	8.617 Å²	-0 Å²
3-	-	-	-5.6619 Å²

Refinement step

Cycle: LAST / Resolution: 2→49.653 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	40308	0	0	3833	44141

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.007	41109
X-RAY DIFFRACTION	f_angle_d	1.028	55482
X-RAY DIFFRACTION	f_chiral_restr	0.071	6031
X-RAY DIFFRACTION	f_plane_restr	0.005	7331
X-RAY DIFFRACTION	f_dihedral_angle_d	14.056	14996

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 26

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Num. reflection all	% reflection obs (%)
2-2.0263	0.2697	103	0.2259	11417	11520	82
2.0263-2.0541	0.3219	148	0.2301	13362	13510	95
2.0541-2.0834	0.2585	148	0.2244	13940	14088	100
2.0834-2.1145	0.2889	132	0.2118	13970	14102	100
2.1145-2.1476	0.2906	160	0.2025	13914	14074	100
2.1476-2.1828	0.2454	160	0.1903	13937	14097	100
2.1828-2.2204	0.2394	151	0.1868	13915	14066	100
2.2204-2.2608	0.2711	146	0.183	14016	14162	100
2.2608-2.3043	0.2874	107	0.1888	13971	14078	100
2.3043-2.3513	0.261	147	0.1889	14015	14162	100
2.3513-2.4024	0.2464	121	0.18	13927	14048	100
2.4024-2.4583	0.2523	116	0.1806	13987	14103	100
2.4583-2.5198	0.2452	163	0.1795	13999	14162	100
2.5198-2.5879	0.2161	133	0.1671	13995	14128	100
2.5879-2.6641	0.2037	141	0.1685	13959	14100	100
2.6641-2.75	0.2246	136	0.1657	13989	14125	100
2.75-2.8483	0.2198	135	0.1756	14020	14155	100
2.8483-2.9624	0.2395	145	0.1801	13985	14130	100
2.9624-3.0972	0.2669	152	0.181	13984	14136	100
3.0972-3.2604	0.2333	131	0.1807	14050	14181	100
3.2604-3.4646	0.227	173	0.1769	13942	14115	100
3.4646-3.7321	0.2108	131	0.1749	14033	14164	100
3.7321-4.1075	0.1649	132	0.1664	14004	14136	100
4.1075-4.7014	0.2246	146	0.1614	14033	14179	100
4.7014-5.9218	0.2169	139	0.1872	14002	14141	99
5.9218-49.6836	0.2022	150	0.1973	14115	14265	99

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	0.8919	-0.1837	0.1006	0.5088	-0.2519	0.867	-0.0382	0.1284	-0.0876	-0.0413	-0.025	-0.0177	0.0893	0.0746	0.058	0.1255	-0.0257	0.0328	0.1537	-0.012	0.1424	24.3164	-8.6008	67.4544
2	1.2157	-0.1172	-0.6346	1.6452	0.7292	2.8642	-0.0447	-0.0266	-0.0791	-0.1659	-0.0187	-0.148	0.2265	0.3779	0.0733	0.1473	0.036	0.0444	0.3322	0.0503	0.1503	52.1018	-17.3884	54.6175
3	1.108	-0.6783	-0.6234	1.4249	0.3665	1.3162	-0.083	-0.0651	-0.0276	-0.0176	-0.0509	-0.1625	0.1275	0.4246	0.1193	0.1145	-0.0207	-0.0087	0.3185	0.0591	0.1651	44.3153	-7.9954	72.5358
4	1.0476	-0.0051	0.085	1.1695	-0.3725	1.0192	-0.0732	-0.1395	0.1134	0.2136	0.0206	0.0335	-0.2343	-0.0874	0.0567	0.2095	0.0412	-0.0486	0.1478	-0.0354	0.1456	5.2985	26.2642	94.0436
5	1.269	-0.9285	-0.673	1.5688	0.3226	2.1367	0.0983	-0.1087	0.1321	0.0849	-0.0225	0.2346	-0.5355	-0.4405	-0.0592	0.2195	0.0504	0.0133	0.2933	-0.0418	0.2382	-16.4426	31.7015	102.4225
6	1.1646	-0.0343	0.0705	0.5394	-0.0244	0.7894	-0.0546	0.0564	-0.2063	-0.0237	0.007	0.0903	0.1027	-0.152	0.0326	0.1129	-0.0403	0.0248	0.1316	-0.0203	0.1529	0.528	-8.982	77.2231
7	1.6198	0.0444	-0.1222	1.2062	0.2904	1.2922	-0.1394	-0.2364	-0.5263	0.4979	-0.0855	0.4369	0.6964	-0.6008	0.0887	0.1519	-0.1757	0.1293	0.4239	0.0095	0.33	-21.8888	-14.3344	81.9745
8	0.9382	-0.0246	0.0077	0.6414	0.3652	0.7868	-0.0896	0.2242	0.1626	-0.2202	-0.0122	-0.0564	-0.3207	0.1042	0.0914	0.2831	-0.0871	-0.0595	0.2172	0.1063	0.2044	22.3333	28.6697	55.3926
9	1.1269	1.3306	-0.2335	1.8678	-0.0351	1.6447	-0.0593	0.0797	0.0336	-0.2417	0.0291	-0.1353	-0.4898	0.1523	0.0079	0.2308	-0.0599	-0.0104	0.2837	0.1367	0.2306	44.637	34.5704	48.0417
10	0.8763	-0.0652	0.0774	0.3354	-0.177	0.7038	-0.0948	-0.0454	0.1887	0.1091	-0.0304	-0.1056	-0.2342	0.1419	0.0987	0.1912	-0.0651	-0.0784	0.1599	0.0225	0.1526	33.2932	20.4027	93.3912
11	1.0154	-0.4515	1.0181	0.4744	-0.412	1.4624	-0.2417	0.1291	0.2819	0.1868	0.0521	-0.0992	-0.2914	0.2689	0.1583	0.2254	-0.0985	-0.0599	0.2397	0.0595	0.2169	50.9963	20.9012	97.1363
12	1.0838	-0.2687	0.0772	0.4776	-0.0427	0.4192	-0.0786	0.1843	0.1573	-0.0912	-0.0336	0.0146	-0.2189	-0.0363	0.1067	0.2028	-0.0039	-0.066	0.205	0.0361	0.1351	-2.9146	23.7204	55.732
13	1.7364	0.6563	0.5333	2.6281	0.4077	3.347	-0.051	0.1439	-0.0215	-0.3109	0.0878	0.1427	0.0915	-0.2025	-0.0456	0.1972	0.0436	-0.084	0.2651	-0.0113	0.1745	-30.2541	15.8984	43.8861
14	1.8133	-1.4433	1.7175	3.2201	-2.5915	3.9965	-0.1628	0.0923	0.3071	-0.0699	-0.0683	-0.077	-0.3503	-0.0541	0.229	0.1623	0.0156	-0.0641	0.1634	-0.0195	0.2074	-20.9691	27.5144	51.3863
15	2.1597	0.8211	0.6622	0.5498	0.0664	0.6772	-0.0759	-0.191	0.3172	-0.0967	-0.0971	0.1192	-0.1968	-0.1525	0.1528	0.2723	0.1221	-0.0583	0.2674	-0.0555	0.2212	-17.9154	32.5987	65.1657
16	0.8936	-0.092	0.1323	0.3805	0.0569	1.0049	-0.0815	-0.0624	0.1607	-0.0027	-0.0103	0.0283	-0.2024	-0.1844	0.0703	0.1286	0.0262	-0.0403	0.103	-0.0228	0.1204	51.6105	12.5216	-8.2243
17	0.9383	-0.3057	0.9107	0.4035	-0.3954	2.0045	-0.2422	-0.1346	0.2101	-0.0186	0.0544	0.0449	-0.4841	-0.3683	0.1844	0.237	0.0582	-0.0639	0.2424	-0.0758	0.1882	31.7313	17.3409	-13.7279
18	0.8865	-0.0059	0.0601	0.7285	0.2867	0.6841	-0.0467	-0.2429	-0.1377	0.1594	0.0158	-0.127	0.1782	0.1186	0.0217	0.1678	0.0719	0.0298	0.1923	0.096	0.1568	79.5168	-23.5979	20.1799
19	1.1679	-0.5791	0.3283	1.4329	-0.2126	2.2814	0.0009	-0.1157	-0.2035	0.2079	-0.0452	-0.2931	0.6934	0.2619	0.0463	0.3254	0.0549	-0.0158	0.2399	0.0777	0.2911	95.0835	-27.6789	27.9957
20	0.9694	-0.1415	-0.0222	0.5935	0.0003	1.391	-0.0954	-0.0597	0.2109	0.003	0.0056	-0.1229	-0.2921	0.3975	0.0624	0.0486	-0.0393	-0.0758	0.0955	0.0172	0.1068	81.1924	13.0168	2.5383
21	1.3831	0.1683	0.3832	1.2535	-0.1337	1.1467	-0.1421	-0.3659	0.3959	0.362	-0.1094	-0.3543	-0.605	0.6027	0.1553	0.2963	-0.1962	-0.121	0.5795	-0.0132	0.3011	100.491	18.3995	7.6043
22	0.8886	-0.2202	0.3624	0.8841	-0.3863	1.1213	-0.0315	0.1487	-0.147	-0.175	-0.0408	0.0088	0.2177	0.0612	0.0624	0.1974	-0.0273	0.0591	0.1078	-0.0422	0.178	58.9814	-25.1502	-21.3216
23	0.8331	0.5791	0.7306	0.8016	0.2283	1.3395	0.1422	-0.0205	-0.1129	-0.0303	-0.0315	0.1034	0.357	-0.1731	-0.0818	0.1867	-0.0077	-0.007	0.1338	-0.0616	0.2166	36.6134	-30.7178	-25.47
24	0.9333	0.029	0.0245	0.3463	0.0586	0.6842	-0.0733	-0.1873	-0.1566	0.1007	-0.0464	0.0683	0.1543	-0.1451	0.1127	0.1545	-0.0042	0.0659	0.1968	0.0129	0.1353	49.4587	-17.3837	17.8647
25	0.8674	-0.337	-0.7683	0.4683	0.4684	1.4526	-0.1292	-0.082	-0.1778	0.2044	-0.0897	0.1565	0.2258	-0.3497	0.1773	0.2068	-0.0806	0.0689	0.3502	-0.043	0.1845	28.1574	-16.7994	21.9381
26	0.9185	-0.0515	-0.0804	0.4814	-0.0194	0.5526	-0.0853	0.1571	-0.1757	-0.1342	-0.081	-0.1155	0.1941	0.2141	0.0855	0.1281	0.0652	0.1072	0.1285	0.0071	0.1269	82.8966	-20.1103	-19.3753
27	1.3478	0.6464	-0.9174	0.9972	-0.2395	1.2655	-0.2264	0.0781	-0.2534	-0.3186	0.0512	-0.2229	0.1689	0.186	0.1142	0.2042	0.0615	0.0873	0.289	0.058	0.2508	104.0556	-20.3499	-23.5439

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	chain 'A' and (resseq 6:209)	A	6 - 209
2	X-RAY DIFFRACTION	2	chain 'A' and (resseq 210:352)	A	210 - 352
3	X-RAY DIFFRACTION	3	chain 'A' and (resseq 353:447)	A	353 - 447
4	X-RAY DIFFRACTION	4	chain 'B' and (resseq 6:209)	B	6 - 209
5	X-RAY DIFFRACTION	5	chain 'B' and (resseq 210:447)	B	210 - 447
6	X-RAY DIFFRACTION	6	chain 'C' and (resseq 6:225)	C	6 - 225
7	X-RAY DIFFRACTION	7	chain 'C' and (resseq 226:447)	C	226 - 447
8	X-RAY DIFFRACTION	8	chain 'D' and (resseq 6:209)	D	6 - 209
9	X-RAY DIFFRACTION	9	chain 'D' and (resseq 210:447)	D	210 - 447
10	X-RAY DIFFRACTION	10	chain 'E' and (resseq 6:253)	E	6 - 253
11	X-RAY DIFFRACTION	11	chain 'E' and (resseq 254:447)	E	254 - 447
12	X-RAY DIFFRACTION	12	chain 'F' and (resseq 6:226)	F	6 - 226
13	X-RAY DIFFRACTION	13	chain 'F' and (resseq 227:316)	F	227 - 316
14	X-RAY DIFFRACTION	14	chain 'F' and (resseq 317:394)	F	317 - 394
15	X-RAY DIFFRACTION	15	chain 'F' and (resseq 395:447)	F	395 - 447
16	X-RAY DIFFRACTION	16	chain 'G' and (resseq 6:241)	G	6 - 241
17	X-RAY DIFFRACTION	17	chain 'G' and (resseq 242:447)	G	242 - 447
18	X-RAY DIFFRACTION	18	chain 'H' and (resseq 6:254)	H	6 - 254
19	X-RAY DIFFRACTION	19	chain 'H' and (resseq 255:447)	H	255 - 447
20	X-RAY DIFFRACTION	20	chain 'I' and (resseq 6:241)	I	6 - 241
21	X-RAY DIFFRACTION	21	chain 'I' and (resseq 242:447)	I	242 - 447
22	X-RAY DIFFRACTION	22	chain 'J' and (resseq 6:187)	J	6 - 187
23	X-RAY DIFFRACTION	23	chain 'J' and (resseq 188:447)	J	188 - 447
24	X-RAY DIFFRACTION	24	chain 'K' and (resseq 6:226)	K	6 - 226
25	X-RAY DIFFRACTION	25	chain 'K' and (resseq 227:447)	K	227 - 447
26	X-RAY DIFFRACTION	26	chain 'L' and (resseq 6:226)	L	6 - 226
27	X-RAY DIFFRACTION	27	chain 'L' and (resseq 227:447)	L	227 - 447

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