PDB-2okg: Structure of effector binding domain of central glycolytic gene r...

ID or keywords:

Entry

Database: PDB / ID: 2okg

Title

Structure of effector binding domain of central glycolytic gene regulator (CggR) from B. subtilis

Components

Central glycolytic gene regulator

Keywords

TRANSCRIPTION / alpha/beta/alpha sandwich / Rossmann-like fold /

Structural Genomics / PSI-2 /

Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG

Function / homology

Function and homology information

carbohydrate binding /

Biological species

Bacillus subtilis (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 1.65 Å

Authors

Rezacova, P. / Moy, S.F. / Joachimiak, A. / Otwinowski, Z. / Midwest Center for Structural Genomics (MCSG)

Citation

Journal: Mol.Microbiol. / Year: 2008
Title: Crystal structures of the effector-binding domain of repressor Central glycolytic gene Regulator from Bacillus subtilis reveal ligand-induced structural changes upon binding of several glycolytic intermediates.
Authors: Rezacova, P. / Kozisek, M. / Moy, S.F. / Sieglova, I. / Joachimiak, A. / Machius, M. / Otwinowski, Z.

History

Deposition	Jan 16, 2007	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jan 30, 2007	Provider: repository / Type: Initial release
Revision 1.1	May 1, 2008	Group: Version format compliance
Revision 1.2	Jul 13, 2011	Group: Version format compliance
Revision 1.3	Dec 27, 2023	Group: Data collection / Database references / Derived calculations Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn / 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_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

Remark 300

BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 2 CHAIN(S) ...

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	2okg.cif.gz	123.9 KB	Display	PDBx/mmCIF format
PDB format	pdb2okg.ent.gz	98 KB	Display	PDB format
PDBx/mmJSON format	2okg.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ok/2okg ftp://data.pdbj.org/pub/pdb/validation_reports/ok/2okg	HTTPS FTP

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Related structure data

Related structure data	3bxeC 3bxfC 3bxgC 3bxhC C: citing same article (ref.)
Similar structure data	4daj-1 3s94-2 4uaf-d 6xt1-4 5kdu-d 6xsz-4 3ap2-d 4daj-4 3ap1-d 4rn6-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
Other databases	TargetDB: APC85550

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#50 - Feb 2004 Glycolytic Enzymes similarity (1)

Deposited unit

A: Central glycolytic gene regulator

B: Central glycolytic gene regulator

hetero molecules

56.1 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: Central glycolytic gene regulator

hetero molecules

B: Central glycolytic gene regulator

hetero molecules

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

Unit cell

Length a, b, c (Å)	52.603, 83.804, 116.721
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

Details

dimer in asymmetric unit is presumably biological relevant unit

#1: Protein	Central glycolytic gene regulator Mass: 27935.668 Da / Num. of mol.: 2 / Fragment: C-terminal domain, residues 89-340 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus subtilis (bacteria) / Strain: 168 / Gene: cggR / Plasmid: pMCSG7 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: O32253
#2: Chemical	ChemComp-CL / CHLORIDE ION / Chloride Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#3: Chemical	ChemComp-G3H / GLYCERALDEHYDE-3-PHOSPHATE / Glyceraldehyde 3-phosphate Mass: 170.058 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₃H₇O₆P
#4: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 472 / 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: 2.3 Å³/Da / Density % sol: 46.56 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: Reservoir: 16% PEG3350, 0.1M MES pH 6.5, 0.1M MgCl2, 0.1M 6-aminohexanoic acid. Protein: 26.2mg/ml. Drops: 1+1 microliter, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.979 Å
Detector	Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 11, 2006
Radiation	Monochromator: Rosenbaum-Rock high-resolution double-crystal, Si 111 Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.979 Å / Relative weight: 1
Reflection	Resolution: 1.65→50 Å / Num. obs: 62805 / % possible obs: 97.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.3 % / B_iso Wilson estimate: 23 Å² / R_merge(I) obs: 0.087 / Net I/σ(I): 52.2
Reflection shell	Resolution: 1.65→1.66 Å / Redundancy: 4.6 % / R_merge(I) obs: 0.627 / Mean I/σ(I) obs: 3.6 / % possible all: 99.2

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Processing

Software

Name	Version	Classification
REFMAC	5.2.0019	refinement
HKL-3000		data collection
HKL-3000		data reduction
HKL-3000		data scaling
MLPHARE		phasing

Refinement

Method to determine structure:

SAD / Resolution: 1.65→34.04 Å / Cor.coef. F_o:F_c: 0.955 / Cor.coef. F_o:F_c free: 0.932 / SU B: 4.799 / SU ML: 0.083 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.111 / ESU R Free: 0.113 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.23871	3089	5.1 %	RANDOM
R_work	0.19575	-	-	-
obs	0.19792	57112	95.96 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK

Displacement parameters

B_iso mean: 18.54 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.36 Å²	0 Å²	0 Å²
2-	-	0.04 Å²	0 Å²
3-	-	-	-0.4 Å²

Refinement step

Cycle: LAST / Resolution: 1.65→34.04 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3882	0	13	472	4367

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.016	0.022	3964
X-RAY DIFFRACTION	r_angle_refined_deg	1.479	1.98	5369
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.389	5	539
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	34.903	25.125	160
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	13.711	15	753
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	15.991	15	23
X-RAY DIFFRACTION	r_chiral_restr	0.105	0.2	623
X-RAY DIFFRACTION	r_gen_planes_refined	0.006	0.02	2919
X-RAY DIFFRACTION	r_nbd_refined	0.216	0.2	1907
X-RAY DIFFRACTION	r_nbtor_refined	0.303	0.2	2758
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.164	0.2	367
X-RAY DIFFRACTION	r_symmetry_vdw_refined	0.191	0.2	47
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.177	0.2	27
X-RAY DIFFRACTION	r_mcbond_it	0.877	1.5	2633
X-RAY DIFFRACTION	r_mcangle_it	1.257	2	4104
X-RAY DIFFRACTION	r_scbond_it	2.214	3	1483
X-RAY DIFFRACTION	r_scangle_it	3.335	4.5	1248

LS refinement shell

Resolution: 1.65→1.694 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.29	232	-
R_work	0.231	4185	-
obs	-	4185	96.89 %

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	27.5194	-1.0926	-7.2675	65.2198	2.5086	9.9274	0.475	-0.6872	-0.7796	0.5928	-0.4397	-1.5905	-0.7893	0.2843	-0.0353	0.2437	-0.0377	0.1023	0.0194	0.0072	0.2538	37.7781	104.1525	26.5654
2	1.4303	1.6901	-1.3054	2.347	-0.4665	4.4992	0.026	-0.2189	0.24	0.2548	-0.0763	0.6433	-0.0277	-0.0794	0.0503	0.0973	0.0233	0.0885	0.037	-0.0435	0.165	36.1811	93.3164	22.0984
3	7.7791	-3.6384	3.3849	4.1969	-1.4662	3.1867	-0.1757	0.0628	0.1724	0.1412	0.0439	0.2047	-0.2856	0.2053	0.1318	0.0876	-0.0365	-0.0102	0.0343	0.0116	0.0039	49.0314	94.9642	14.6381
4	5.1488	0.1635	0.4175	1.7752	1.5405	1.4674	0.0445	0.287	0.2477	-0.2199	0.0234	0.1186	-0.2271	0.2158	-0.0679	0.0517	-0.012	-0.0082	0.0516	0.0089	-0.0592	48.8047	89.0333	7.0734
5	1.9703	-0.086	-0.1526	2.5548	0.0997	2.3151	-0.0835	0.203	0.2682	0.1615	0.0786	-0.0687	-0.0677	0.3654	0.0048	0.0762	-0.0187	0.0036	0.1331	-0.0197	-0.0112	56.4334	87.5314	9.4153
6	22.1784	28.89	-16.1214	41.6485	-23.3847	13.1347	-2.6349	2.059	1.2236	-2.7912	4.2119	3.0384	-0.6943	1.1172	-1.577	0.2926	-0.0884	-0.1329	0.4461	-0.0024	0.3469	43.9076	79.5352	-7.0145
7	2.7045	-0.4581	-0.9368	4.2811	3.6256	5.6226	0.0497	0.2104	0.1938	-0.428	-0.0233	-0.0004	-0.5866	0.1271	-0.0264	0.1391	-0.0166	0.0006	0.1531	0.0025	-0.0152	55.799	87.6209	2.1845
8	2.0314	1.1352	-0.5357	5.4456	3.5154	4.2381	-0.1179	-0.1635	-0.2942	0.377	-0.0082	0.2185	0.2891	0.0238	0.1261	0.1143	-0.0051	0.042	0.0615	0.0066	0.0436	50.1278	68.5263	-5.916
9	1.9312	0.951	-0.0088	1.4426	0.4688	2.0796	-0.2412	0.035	-0.0584	-0.0006	0.2664	-0.1477	0.2613	0.3039	-0.0252	0.0921	0.0116	-0.0036	0.0445	0.0025	-0.0356	51.8261	76.8985	7.5992
10	17.0994	0.5426	-15.0821	18.2725	-3.0164	42.1675	-0.5551	1.8293	1.2322	-1.2967	0.1931	0.223	-0.847	-0.9227	0.362	0.2325	-0.1019	-0.1161	0.2907	0.136	0.1431	32.4755	82.1949	-0.8773
11	2.3406	0.1839	1.5805	3.2505	0.9458	2.8111	0.028	0.1797	0.1417	-0.2804	-0.0656	0.1014	0.2163	-0.1367	0.0377	0.0742	-0.0408	-0.0075	0.0518	0.0175	0.0021	31.2589	74.4184	5.6696
12	0.7607	0.4689	0.385	0.4413	1.6187	12.7246	-0.0185	0.0113	-0.5444	0.0404	0.0252	-0.2133	0.6724	0.2902	-0.0067	0.1573	0.0066	0.0059	0.1058	-0.0448	0.153	45.2256	72.0404	8.2469
13	4.0402	1.3504	-0.4575	1.956	0.7459	2.3416	0.1165	-0.1606	0.0908	0.1678	-0.1192	0.2982	0.119	-0.0889	0.0027	0.0304	-0.0134	0.0096	-0.0165	-0.0127	0.0133	38.1696	85.2618	17.0139
14	19.4461	10.4063	-8.5361	34.9677	-15.0703	9.7125	1.0995	-0.3741	1.7561	1.8565	-0.613	3.9037	-0.7171	-0.7239	-0.4866	0.1684	0.0342	0.1864	0.176	-0.0606	0.5349	27.4587	94.1231	20.7978
15	0.0364	-0.9307	-0.2988	23.859	6.9195	9.0632	-0.1264	-0.2092	0.0488	-0.796	-0.2765	0.8801	-0.6553	-0.0458	0.4029	0.2213	-0.0818	0.0023	0.2185	0.0417	0.3176	76.1855	103.2426	-26.2521
16	4.8004	-1.7768	-2.3127	4.2537	2.2669	10.5709	0.2115	0.0834	1.014	-0.289	0.2269	-0.5046	-0.0384	0.5003	-0.4385	0.0471	-0.0364	0.0625	0.0157	-0.0135	0.2847	74.5368	95.0498	-21.8113
17	5.4214	1.4742	4.0152	2.5903	1.8638	8.2052	0.1532	0.161	0.6438	-0.2372	0.0386	-0.0155	-0.1553	-0.0167	-0.1919	0.0508	0.0091	0.0561	-0.0189	0.0408	0.2464	62.4073	97.1434	-20.2757
18	5.0461	0.7214	1.4086	2.7111	0.7969	2.855	0.1025	0.03	0.3799	-0.012	-0.0315	0.0324	0.0447	-0.2664	-0.071	0.0085	-0.0053	0.0124	0.0306	0.0056	-0.0052	57.6603	87.5847	-19.7888
19	5.1503	0.3655	0.2797	2.0163	0.5268	2.0392	0.007	0.1882	0.8975	-0.3032	-0.1068	0.2435	-0.3556	-0.38	0.0998	0.1061	0.0412	0.004	0.0882	0.0415	0.1612	51.7964	92.6066	-20.9559
20	6.8386	-1.6002	0.0468	1.951	0.685	3.937	0.0214	-0.3741	-0.3075	0.0884	-0.0408	-0.1021	0.442	-0.0576	0.0194	0.1034	-0.0305	0.0171	0.0652	0.0321	-0.0073	61.6663	77.7754	-11.0132
21	4.8559	-1.7882	0.3948	6.3857	-2.5115	2.0535	0.071	-0.1657	0.2091	0.0894	-0.0254	0.2441	-0.0725	-0.1093	-0.0456	0.0453	-0.0029	0.0074	0.0964	-0.0354	-0.0184	51.318	84.3191	-14.2018
22	6.4123	-4.2528	2.7861	9.8538	-3.0845	4.3216	0.0955	0.3975	0.3084	-0.1619	-0.309	-0.3091	0.0504	0.2018	0.2135	0.0868	0.022	0.0386	0.0179	0.0334	0.0863	55.488	63.1249	-14.0426
23	5.434	0.8759	0.2157	1.1941	-0.0346	1.1363	-0.0985	0.3788	-0.2502	-0.0566	0.1619	0.0834	0.0222	-0.1085	-0.0635	0.0292	-0.0071	-0.0073	0.0563	-0.0264	-0.0145	55.503	77.9024	-23.3041
24	9.9024	-2.6644	-0.0006	5.7766	-0.5863	6.8701	-0.0916	-0.6296	-0.5437	0.2993	0.1026	0.2876	0.8387	0.2529	-0.0109	0.2563	0.1056	-0.0247	0.1705	0.0462	0.0079	73.8074	73.6998	-8.8437
25	3.5721	-0.5784	0.0265	5.9696	0.0652	2.409	-0.1767	-0.1653	-0.2425	0.2284	0.1256	-0.0516	0.377	0.1923	0.0512	0.1104	0.0565	0.0229	0.056	-0.0129	-0.0208	74.9574	73.3022	-18.8848
26	5.7878	-0.481	-0.345	2.2424	1.1596	2.0232	-0.0402	0.5569	-0.27	-0.2729	0.0144	-0.011	0.1148	-0.1241	0.0258	0.0711	-0.0253	0.0015	0.0957	0.0111	-0.0026	63.3632	80.471	-27.0782
27	5.496	-0.8965	-0.7469	2.6012	1.4743	3.933	0.0247	0.1359	0.6166	-0.0259	0.1441	-0.2338	0.0832	0.2792	-0.1687	0.0174	-0.011	0.0172	0.0177	-0.002	0.0223	75.2219	87.133	-22.9278
28	11.873	-4.5531	-8.9498	21.0548	5.7394	17.9754	0.3852	-0.4501	1.9964	0.2757	0.0052	-0.5361	-0.5529	0.4104	-0.3904	-0.0341	-0.0678	0.0172	0.0733	-0.15	0.3719	81.8628	95.7513	-19.1502

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	X-RAY DIFFRACTION	1	A	A	89 - 93	4 - 8
2	X-RAY DIFFRACTION	2	A	A	94 - 120	9 - 35
3	X-RAY DIFFRACTION	3	A	A	121 - 142	36 - 57
4	X-RAY DIFFRACTION	4	A	A	143 - 158	58 - 73
5	X-RAY DIFFRACTION	5	A	A	159 - 178	74 - 93
6	X-RAY DIFFRACTION	6	A	A	179 - 184	94 - 99
7	X-RAY DIFFRACTION	7	A	A	185 - 203	100 - 118
8	X-RAY DIFFRACTION	8	A	A	204 - 221	119 - 136
9	X-RAY DIFFRACTION	9	A	A	222 - 243	137 - 158
10	X-RAY DIFFRACTION	10	A	A	244 - 252	159 - 167
11	X-RAY DIFFRACTION	11	A	A	253 - 285	168 - 200
12	X-RAY DIFFRACTION	12	A	A	286 - 295	201 - 210
13	X-RAY DIFFRACTION	13	A	A	296 - 333	211 - 248
14	X-RAY DIFFRACTION	14	A	A	334 - 338	249 - 253
15	X-RAY DIFFRACTION	15	B	B	88 - 102	3 - 17
16	X-RAY DIFFRACTION	16	B	B	103 - 121	18 - 36
17	X-RAY DIFFRACTION	17	B	B	122 - 139	37 - 54
18	X-RAY DIFFRACTION	18	B	B	140 - 156	55 - 71
19	X-RAY DIFFRACTION	19	B	B	157 - 174	72 - 89
20	X-RAY DIFFRACTION	20	B	B	175 - 186	90 - 101
21	X-RAY DIFFRACTION	21	B	B	187 - 206	102 - 121
22	X-RAY DIFFRACTION	22	B	B	207 - 221	122 - 136
23	X-RAY DIFFRACTION	23	B	B	222 - 242	137 - 157
24	X-RAY DIFFRACTION	24	B	B	243 - 259	158 - 174
25	X-RAY DIFFRACTION	25	B	B	260 - 287	175 - 202
26	X-RAY DIFFRACTION	26	B	B	288 - 305	203 - 220
27	X-RAY DIFFRACTION	27	B	B	306 - 329	221 - 244
28	X-RAY DIFFRACTION	28	B	B	330 - 338	245 - 253

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Yorodumi