PDB-3sbo: Structure of E.coli GDH from native source

ID or keywords:

Entry

Database: PDB / ID: 3sbo

Title

Structure of E.coli GDH from native source

Components

NADP-specific glutamate dehydrogenase

Keywords

OXIDOREDUCTASE / Rossmann fold / Dehydrogenase

Function / homology

Function and homology information

glutamate dehydrogenase complex / glutamate dehydrogenase (NADP+) / glutamate biosynthetic process / glutamate metabolic process / glutamate dehydrogenase (NADP+) activity / guanosine tetraphosphate binding / identical protein binding / cytoplasm / cytosol
Similarity search - Function

Biological species

Escherichia coli (E. coli)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 3.204 Å

Authors

Gee, C.L. / Zubieta, C. / Echols, N. / Totir, M.

Citation

Journal: Plos One / Year: 2012
Title: Macro-to-Micro Structural Proteomics: Native Source Proteins for High-Throughput Crystallization.
Authors: Totir, M. / Echols, N. / Nanao, M. / Gee, C.L. / Moskaleva, A. / Gradia, S. / Iavarone, A.T. / Berger, J.M. / May, A.P. / Zubieta, C. / Alber, T.

History

Deposition	Jun 6, 2011	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Mar 21, 2012	Provider: repository / Type: Initial release
Revision 1.1	Nov 12, 2014	Group: Structure summary
Revision 1.2	Nov 8, 2017	Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software
Revision 1.3	Feb 28, 2024	Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_unobs_or_zero_occ_atoms / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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	3sbo.cif.gz	916.1 KB	Display	PDBx/mmCIF format
PDB format	pdb3sbo.ent.gz	770.6 KB	Display	PDB format
PDBx/mmJSON format	3sbo.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	3sbo_validation.pdf.gz	485.3 KB	Display	wwPDB validaton report
Full document	3sbo_full_validation.pdf.gz	532.6 KB	Display
Data in XML	3sbo_validation.xml.gz	91.1 KB	Display
Data in CIF	3sbo_validation.cif.gz	120.8 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/sb/3sbo ftp://data.pdbj.org/pub/pdb/validation_reports/sb/3sbo	HTTPS FTP

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Related structure data

Related structure data	2xhyC 3n6qC 3nbuC C: citing same article (ref.)
Similar structure data	4fcc-1 4bht-d 4fcc-2 4fhn-3 6yeh-d 2tmg-d 6yei-d 3aoe-d 3aog-2 1euz-d 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: NADP-specific glutamate dehydrogenase

B: NADP-specific glutamate dehydrogenase

C: NADP-specific glutamate dehydrogenase

D: NADP-specific glutamate dehydrogenase

E: NADP-specific glutamate dehydrogenase

F: NADP-specific glutamate dehydrogenase

hetero molecules

292 kDa, 6 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)	101.922, 151.617, 169.970
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Protein	NADP-specific glutamate dehydrogenase / NADP-GDH Mass: 48635.215 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: DH5alpha References: UniProt: P00370, glutamate dehydrogenase (NADP+)
#2: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Cl
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 44 / 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: 2.25 Å³/Da / Density % sol: 45.34 %
Crystal grow	Temperature: 293 K / Method: liquid diffusion / pH: 7.5 Details: 0.2M NaCl, 0.1 HEPES pH 7.5, 25% w/v PEG 3350, LIQUID DIFFUSION, temperature 293K

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.92001 Å
Detector	Type: MARMOSAIC 325 mm CCD / Detector: CCD / Date: May 27, 2008 / Details: DCM S111
Radiation	Monochromator: DCM S111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.92001 Å / Relative weight: 1
Reflection	Resolution: 3.2→40 Å / Num. obs: 43926 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.7 % / R_sym value: 0.164 / Net I/σ(I): 7.9
Reflection shell	Resolution: 3.2→3.31 Å / Redundancy: 3.6 % / Mean I/σ(I) obs: 2.25 / Num. unique all: 4309 / R_sym value: 0.515 / % possible all: 99.7

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Processing

Software

Name	Version	Classification
MOSFLM		data reduction
PHASER		phasing
PHENIX	(phenix.refine: 1.7_650)	refinement
HKL-2000		data reduction
HKL-2000		data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 3.204→37.971 Å / SU ML: 0.41 / σ(F): 1.34 / Phase error: 27.29 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2653	2204	5.03 %	RANDOM
R_work	0.2286	-	-	-
obs	0.2305	43835	99.73 %	-
all	-	43926	-	-

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / B_sol: 20.038 Å² / k_sol: 0.277 e/Å³

Displacement parameters

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-11.3137 Å²	-0 Å²	-0 Å²
2-	-	-17.7664 Å²	0 Å²
3-	-	-	-12.4131 Å²

Refinement step

Cycle: LAST / Resolution: 3.204→37.971 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	19913	0	8	44	19965

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.001	20293
X-RAY DIFFRACTION	f_angle_d	0.424	27398
X-RAY DIFFRACTION	f_dihedral_angle_d	9.517	7326
X-RAY DIFFRACTION	f_chiral_restr	0.03	3001
X-RAY DIFFRACTION	f_plane_restr	0.002	3611

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 (%)
3.2044-3.3189	0.3808	198	0.3221	4095	X-RAY DIFFRACTION	99
3.3189-3.4517	0.3187	197	0.3005	4112	X-RAY DIFFRACTION	99
3.4517-3.6086	0.3397	223	0.2776	4095	X-RAY DIFFRACTION	100
3.6086-3.7987	0.2874	227	0.255	4125	X-RAY DIFFRACTION	100
3.7987-4.0365	0.2601	213	0.2251	4108	X-RAY DIFFRACTION	100
4.0365-4.3477	0.2383	230	0.1984	4138	X-RAY DIFFRACTION	100
4.3477-4.7845	0.2291	218	0.1878	4174	X-RAY DIFFRACTION	100
4.7845-5.4751	0.267	200	0.2066	4215	X-RAY DIFFRACTION	100
5.4751-6.8913	0.2782	237	0.2275	4214	X-RAY DIFFRACTION	100
6.8913-37.9732	0.2043	261	0.1912	4355	X-RAY DIFFRACTION	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	0.0254	-0.0079	-0.0097	0.0383	0.0077	0.0028	-0.072	0.0698	-0.064	0.0096	0.0708	0.0081	-0.0051	-0.0035	0.0022	0.2361	-0.1518	-0.0421	0.0827	-0.0672	-0.0001	70.485	54.0953	59.8947
2	0.58	-0.0941	-0.0983	0.4959	-0.1256	0.0423	0.1094	0.2079	0.0339	-0.331	0.0966	-0.0228	0.1038	-0.06	-0.1417	0.2656	0.0224	0.017	0.2842	-0.045	0.112	93.654	54.3612	47.5536
3	0.0038	0.0015	-0.0062	0.0044	-0.0065	0.017	-0.0458	-0.027	0.0896	-0.0002	0.0643	-0.0144	0.0293	-0.0366	-0.0069	0.0913	-0.093	-0.0363	0.1683	-0.2095	0.1091	90.6761	47.8591	57.5874
4	0.0052	-0.0355	-0.0214	0.0102	0.0149	0.0238	-0.0096	0.0581	-0.0258	0.0131	0.0082	-0.035	0.0168	0.0336	0.002	-0.0282	0.0644	0.2576	-0.0522	-0.2636	-0.1824	57.146	95.954	60.321
5	0.0073	-0.006	-0.0172	0.0065	0.0129	0.0318	0.0398	-0.0186	-0.0253	-0.0475	0.0229	-0.0241	-0.0037	0.023	-0.014	-0.0377	0.2862	0.101	0.302	-0.2243	0.0588	30.829	99.697	48.055
6	0.4307	-0.1461	-0.2071	0.0513	0.0603	0.1074	0.1244	-0.1214	0.1059	-0.0026	0.057	-0.0689	0.0199	0.1142	-0.1801	0.3255	0.0886	-0.1063	0.3854	-0.1192	0.39	37.48	105.231	55.783
7	0.123	0.0428	-0.0209	0.0413	0.0437	0.1249	-0.1322	-0.0108	0.0508	0.0009	0.1058	0.0525	-0.0388	-0.0209	0.034	0.1213	0.1402	0.0414	0.0827	0.1204	0.2028	49.897	57.533	65.002
8	0.5845	0.1374	-0.1591	0.0344	-0.0017	0.4578	0.0512	-0.0882	-0.2852	0.022	-0.0154	-0.0257	-0.0762	-0.065	-0.0191	0.3097	0.1631	0.061	0.467	0.1683	0.4	22.756	54.656	72.864
9	0.146	0.0832	-0.0377	0.0527	-0.0317	0.1993	-0.0352	-0.0009	-0.0823	0.0189	0.0605	-0.0093	-0.1339	-0.1011	0.0009	0.1875	0.2186	0.0904	0.1744	0.1755	0.2135	26.474	54.433	65.118
10	0.0735	-0.0072	-0.0131	0.0527	0.0524	0.0878	-0.1199	-0.0456	0.0631	0.016	0.0031	0.0562	-0.0554	0.0044	0.0122	-0.0237	0.2475	-0.1083	-0.0411	-0.049	0.0759	78.702	95.727	62.146
11	0.1544	-0.0768	0.1564	0.1132	-0.0093	0.1874	0.1372	0.0502	-0.107	0.0745	0.113	0.132	-0.0637	-0.0409	-0.1055	0.1347	0.1348	0.0632	0.1841	0.2362	0.3332	101.774	99.553	71.575
12	0.5272	-0.0766	0.0348	0.285	-0.0769	0.024	0.0969	0.0977	-0.0644	0.1337	0.0542	-0.0328	-0.0722	-0.036	-0.105	0.237	0.091	-0.0389	0.2051	0.1052	0.2511	99.618	92.3	61.289
13	0.0189	-0.0061	0.0009	0.0225	-0.0168	0.0022	-0.0138	-0.0544	-0.0034	0.1348	0.1578	-0.0188	0.0742	-0.045	-0.0212	0.1569	0.2035	-0.013	0.0913	-0.0745	0.0508	75.2166	73.0351	98.4479
14	0.0088	0.0012	0.0024	0.0243	-0.0049	0.0051	0.0249	-0.0487	-0.0017	0.0119	0.0558	-0.018	0.0254	0.0594	-0.0169	0.1056	0.1969	-0.1149	0.1854	0.0003	0.0402	96.2498	58.0162	94.2084
15	0.021	-0.0292	-0.0236	0.0687	0.0405	0.0324	-0.0936	-0.1178	-0.0184	0.1878	0.0258	0.0281	0.1393	0.0014	0.0614	0.4489	0.1657	-0.0721	0.4745	0.0193	0.2651	99.7483	64.178	101.3295
16	0.048	0.0018	0.005	0.0196	0.0066	-0.0069	-0.1071	-0.0602	-0.0314	0.0864	0.0854	0.0069	-0.0302	0.0075	0.0085	0.1546	0.1487	-0.0398	0.0898	-0.041	0.0958	55.503	80.951	96.918
17	0.0104	-0.0061	0.002	0.0017	0.009	0.004	-0.0093	0.0025	-0.0057	0.033	-0.0097	-0.0343	0.0201	-0.0098	-0.0018	0.0664	0.1511	-0.1822	-0.0445	-0.0292	0.1615	29.087	96.998	102.129
18	0.0568	-0.026	0.0436	0.0473	-0.0195	0.0363	0.0267	0.0518	0.0691	0.0135	-0.0569	-0.1216	0.0086	0.0332	0.0265	0.1268	0.0621	-0.0893	0.146	-0.0643	0.2933	33.434	84.456	101.305

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	(chain A and resid -11:178)
2	X-RAY DIFFRACTION	2	(chain A and resid 179:317)
3	X-RAY DIFFRACTION	3	(chain A and resid 318:414)
4	X-RAY DIFFRACTION	4	(chain B and resid -20:201)
5	X-RAY DIFFRACTION	5	(chain B and resid 202:302)
6	X-RAY DIFFRACTION	6	(chain B and resid 303:414)
7	X-RAY DIFFRACTION	7	(chain C and resid -14:195)
8	X-RAY DIFFRACTION	8	(chain C and resid 196:291)
9	X-RAY DIFFRACTION	9	(chain C and resid 292:414)
10	X-RAY DIFFRACTION	10	(chain D and resid -21:171)
11	X-RAY DIFFRACTION	11	(chain D and resid 172:332)
12	X-RAY DIFFRACTION	12	(chain D and resid 333:414)
13	X-RAY DIFFRACTION	13	(chain E and resid -24:171)
14	X-RAY DIFFRACTION	14	(chain E and resid 172:289)
15	X-RAY DIFFRACTION	15	(chain E and resid 290:414)
16	X-RAY DIFFRACTION	16	(chain F and resid -26:196)
17	X-RAY DIFFRACTION	17	(chain F and resid 197:317)
18	X-RAY DIFFRACTION	18	(chain F and resid 318:414)

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