PDB-3bxh: Crystal structure of effector binding domain of central glycolyti...

ID or keywords:

Entry

Database: PDB / ID: 3bxh

Title

Crystal structure of effector binding domain of central glycolytic gene regulator (CggR) from Bacillus subtilis in complex with fructose-6-phosphate

Components

Central glycolytic gene regulator

Keywords

GENE REGULATION / effector binding domain / catabolic repressor / transcriptional regulator / DeoR family / DNA-binding / Transcription regulation

Function / homology

Function and homology information

regulation of DNA-templated transcription initiation / cis-regulatory region sequence-specific DNA binding / carbohydrate binding
Similarity search - Function

Biological species

Bacillus subtilis (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.85 Å

Authors

Rezacova, P. / Otwinowski, Z.

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 13, 2008	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jul 1, 2008	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Advisory / Refinement description / Version format compliance
Revision 1.2	Jul 29, 2020	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_ref_seq_dif / struct_site / struct_site_gen Item: _chem_comp.mon_nstd_flag / _chem_comp.name ..._chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_ref_seq_dif.details Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3	Aug 30, 2023	Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	3bxh.cif.gz	126.5 KB	Display	PDBx/mmCIF format
PDB format	pdb3bxh.ent.gz	99.5 KB	Display	PDB format
PDBx/mmJSON format	3bxh.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	3bxh_validation.pdf.gz	1 MB	Display	wwPDB validaton report
Full document	3bxh_full_validation.pdf.gz	1 MB	Display
Data in XML	3bxh_validation.xml.gz	27.1 KB	Display
Data in CIF	3bxh_validation.cif.gz	41.4 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/bx/3bxh ftp://data.pdbj.org/pub/pdb/validation_reports/bx/3bxh	HTTPS FTP

-
Related structure data

Related structure data	2okgSC 3bxeC 3bxfC 3bxgC S: Starting model for refinement C: citing same article (ref.)
Similar structure data	2vs6-d 3mwp-4 2okg-2 3mx5-2 2bwy-d 3mwt-3 4kkx-d 3aqk-d 7bwy-d 5w4v-2 Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

-
Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#50 - Feb 2004 Glycolytic Enzymes similarity (1) #190 - Oct 2015 Two-component Systems similarity (1)

Deposited unit

A: Central glycolytic gene regulator

B: Central glycolytic gene regulator

hetero molecules

55.8 kDa, 2 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)	55.462, 83.683, 113.747
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

Details

AUTHORS STATE THAT THE DIMERIC ASSEMBLY OF THE BIOLOGICAL UNIT THAT IS SHOWN IN REMARK 350 IS PUTATIVE AT THE TIME OF DEPOSITION.

#1: Protein

Central glycolytic gene regulator

Mass: 27560.508 Da / Num. of mol.: 2 / Fragment: Effector binding domain: Residues 89-340
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Bacillus subtilis (bacteria) / Strain: 168 / Gene: cggR, yvbQ, BSU33950 / Plasmid: pMCSG7 / Production host:

Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O32253

#2: Sugar

ChemComp-F6P / 6-O-phosphono-beta-D-fructofuranose / FRUCTOSE-6-PHOSPHATE / 6-O-phosphono-beta-D-fructose / 6-O-phosphono-D-fructose / 6-O-phosphono-fructose

Type: D-saccharide, beta linking / Mass: 260.136 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C₆H₁₃O₉P

#3: Chemical

ChemComp-SCN / THIOCYANATE ION

Mass: 58.082 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CNS

#4: Water

ChemComp-HOH / water

Mass: 18.015 Da / Num. of mol.: 622 / Source method: isolated from a natural source / Formula: H₂O

-
Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

Crystal	Density Matthews: 2.39 Å³/Da / Density % sol: 48.63 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.6 Details: Reservoir: 0.2M Thiocyanate pH 6.6, 20% (w/v) PEG 3350. 25mg/ml protein with 10mM fructose-6-phosphate, VAPOR DIFFUSION, HANGING DROP, temperature 298K

-
Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.979 Å
Detector	Type: MAR CCD 165 mm / Detector: CCD / Date: Feb 7, 2007
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: 1.85→49.85 Å / Num. obs: 45227 / % possible obs: 97.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 6.3 % / B_iso Wilson estimate: 20.2 Å² / R_sym value: 0.1 / Net I/σ(I): 21.82
Reflection shell	Resolution: 1.85→1.92 Å / Redundancy: 5.5 % / Mean I/σ(I) obs: 3 / % possible all: 97.2

-
Processing

Software

Name	Version	Classification
REFMAC	5.3.0037	refinement
HKL-3000		data collection
HKL-3000		data reduction
HKL-3000		data scaling
MOLREP		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB entry 2OKG

2okg

Resolution: 1.85→49.85 Å / Cor.coef. F_o:F_c: 0.964 / Cor.coef. F_o:F_c free: 0.937 / SU B: 4.567 / SU ML: 0.08 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.132 / ESU R Free: 0.13 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.20965	2284	5.1 %	RANDOM
R_work	0.1609	-	-	-
obs	0.1633	42926	98.7 %	-

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: 20.097 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.98 Å²	0 Å²	0 Å²
2-	-	-0.74 Å²	0 Å²
3-	-	-	-0.24 Å²

Refinement step

Cycle: LAST / Resolution: 1.85→49.85 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3782	0	38	622	4442

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.012	0.022	4060
X-RAY DIFFRACTION	r_bond_other_d
X-RAY DIFFRACTION	r_angle_refined_deg	1.446	1.982	5522
X-RAY DIFFRACTION	r_angle_other_deg
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.042	5	561
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	37.94	25.444	169
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	13.293	15	763
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	12.332	15	21
X-RAY DIFFRACTION	r_chiral_restr	0.098	0.2	640
X-RAY DIFFRACTION	r_gen_planes_refined	0.005	0.02	2999
X-RAY DIFFRACTION	r_gen_planes_other
X-RAY DIFFRACTION	r_nbd_refined	0.231	0.2	2094
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined	0.299	0.2	2805
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.194	0.2	554
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	0.203	0.2	86
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.171	0.2	49
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	0.593	1.5	2584
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it	1.062	2	4173
X-RAY DIFFRACTION	r_scbond_it	1.983	3	1476
X-RAY DIFFRACTION	r_scangle_it	3.379	4.5	1320
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

LS refinement shell

Resolution: 1.85→1.9 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.29	170	-
R_work	0.203	2841	-
obs	-	-	90.58 %

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	2.625	0.2155	-0.1589	3.8356	1.7854	3.794	0.0105	-0.233	-0.1635	0.0793	-0.0438	-0.0901	0.0861	0.0878	0.0332	-0.0493	-0.0014	-0.0077	-0.0075	0.0459	-0.0068	70.547	74.363	76.715
2	5.0625	-2.6171	-1.2964	3.817	0.9604	2.0108	-0.0807	-0.1492	0.0984	0.2201	0.1042	-0.0252	0.0974	-0.1677	-0.0235	0.0133	-0.0122	-0.0076	0.0211	0.0179	0.0007	55.104	78.056	73.362
3	2.3272	-0.2322	-0.1272	2.9582	-0.0084	1.8328	-0.0238	0.0481	-0.2117	0.0301	0.0223	0.0948	0.1734	-0.0314	0.0014	0.0337	-0.0129	-0.0251	0.0041	-0.0097	-0.0152	57.917	77.313	64.451
4	2.4902	0.5255	-0.3086	2.401	-0.5	2.7094	-0.033	0.1901	-0.0767	-0.0798	0.0286	0.1349	0.0295	-0.0362	0.0044	0.0095	0.0029	-0.0217	0.0057	0.0012	-0.0226	55.755	82.825	59.874
5	3.5581	9.0169	-4.3988	23.0618	-12.3538	12.3215	-0.7605	0.1574	-0.4134	-0.8999	0.227	-1.6721	-0.394	0.5237	0.5335	0.1774	-0.0837	-0.0448	0.1602	0.036	0.2397	60.076	98.796	49.708
6	1.4605	-1.5105	0.3488	4.1821	-1.1113	3.5236	-0.0447	0.0036	0.1294	-0.1814	0.134	0.1877	-0.3925	-0.2467	-0.0893	0.0713	0.0069	-0.0193	-0.0131	0.0095	0.0395	54.704	93.958	63.034
7	6.1308	5.0847	-5.3873	7.9824	-6.3395	7.7425	-0.3033	0.2555	0.062	-0.629	0.2024	-0.2565	0.2997	-0.2749	0.1009	0.0268	-0.0322	0.0549	0.0152	-0.0121	-0.0061	78.268	89.004	56.847
8	2.9386	0.9466	-0.0272	3.6065	-1.4956	3.7706	-0.0671	0.0405	0.0399	-0.1234	0.0151	-0.1303	-0.3099	0.135	0.052	0.0162	-0.0547	0.0031	0.0006	0.0009	0.008	77.602	92.828	65.642
9	2.156	0.3547	0.3316	1.235	-0.0068	1.719	-0.0301	-0.0482	0.1166	0.0465	0.0088	-0.0518	-0.1286	0.1341	0.0213	-0.002	-0.032	0.0036	0.0025	-0.0052	-0.0072	69.448	86.65	71.365
10	22.0985	-0.4963	15.3167	13.5992	5.6708	20.3741	0.4738	0.3011	-0.8152	0.2342	0.0591	-0.2868	0.4063	0.222	-0.533	-0.0423	0.0221	-0.032	0.0039	0.0124	0.0489	81.363	74.259	78.348
11	1.2458	0.2764	-0.3711	1.2267	-0.1797	1.1807	-0.0209	-0.0268	-0.1247	-0.0091	0.0105	-0.1099	0.0445	0.0417	0.0104	0.0074	-0.0071	-0.0149	-0.0014	-0.0016	0.0278	48.625	74.263	37.664
12	4.1116	-2.1201	-1.9199	3.0749	1.6334	1.9195	0.0285	-0.2488	-0.0222	0.2269	0.0066	-0.2022	0.0337	0.1289	-0.0351	0.0232	-0.0239	-0.0301	0.0374	-0.0067	-0.0206	52.451	81.484	44.741
13	3.4617	-5.0329	-0.7562	13.3123	3.4268	1.0687	0.049	0.1798	0.0778	-0.2814	-0.0271	-0.0243	-0.2416	-0.2201	-0.0219	0.1069	0.0196	-0.0063	-0.011	-0.007	0.0137	53.162	100.885	42.464
14	1.343	-1.0028	-0.4367	1.698	1.2536	1.232	-0.0504	0.1125	0.0541	-0.2672	0.1598	-0.2997	-0.1416	0.0512	-0.1094	0.019	0.0068	0.0329	0.0048	0.0116	0.0256	51.469	88.321	33.613
15	4.1499	-3.8177	0.4697	12.174	-0.0204	5.5496	-0.1243	-0.1741	0.3449	0.8629	0.214	-0.0584	-0.5889	0.0839	-0.0897	0.1258	-0.0091	0.0749	-0.0323	-0.0228	0.0041	32.886	93.951	47.864
16	2.9613	-0.3823	-0.5949	4.0707	-0.3459	3.453	0.0381	0.0754	0.0933	0.1368	0.1676	0.229	-0.3604	-0.1321	-0.2057	0.0297	0.0398	0.0273	-0.0217	0.0228	0.0195	30.979	92.166	37.876
17	3.7165	-0.5797	-0.0584	7.7899	4.9581	8.2602	0.1153	0.2379	0.339	-0.1719	0.0161	0.1654	-0.5124	-0.2124	-0.1314	0.0172	-0.0057	0.0352	-0.0006	0.0354	0.049	43.268	92.907	31.864
18	1.8668	0.3624	-0.557	1.9091	-0.7118	1.7672	0.0401	0.0771	-0.053	-0.0714	0.0176	0.199	0.0032	-0.1115	-0.0577	-0.0058	-0.0059	-0.0017	0.0014	-0.0006	0.0223	33.754	78.561	34.028

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	93 - 126
2	X-RAY DIFFRACTION	2	A	127 - 143
3	X-RAY DIFFRACTION	3	A	144 - 164
4	X-RAY DIFFRACTION	4	A	165 - 202
5	X-RAY DIFFRACTION	5	A	203 - 220
6	X-RAY DIFFRACTION	6	A	221 - 240
7	X-RAY DIFFRACTION	7	A	241 - 260
8	X-RAY DIFFRACTION	8	A	261 - 285
9	X-RAY DIFFRACTION	9	A	286 - 333
10	X-RAY DIFFRACTION	10	A	334 - 340
11	X-RAY DIFFRACTION	11	B	120 - 178
12	X-RAY DIFFRACTION	12	B	179 - 202
13	X-RAY DIFFRACTION	13	B	203 - 221
14	X-RAY DIFFRACTION	14	B	222 - 242
15	X-RAY DIFFRACTION	15	B	243 - 260
16	X-RAY DIFFRACTION	16	B	261 - 285
17	X-RAY DIFFRACTION	17	B	286 - 296
18	X-RAY DIFFRACTION	18	B	297 - 332

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

Version 3 of the EMDB header file is now the official format.
The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

Thousand views of thousand structures

Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

-Movie

-Structure viewers

+Viewer log

-This page

-This web site

-Options

+Open data

-Basic information

-Structure visualization

-Downloads & links

-Download

-Validation report

-Related structure data

-Links

-Assembly

-Components

-Experimental details

-Experiment

-Sample preparation

-Data collection

-Processing

+About Yorodumi

-News

-Feb 9, 2022. New format data for meta-information of EMDB entries

-Aug 12, 2020. Covid-19 info

+Mar 5, 2020. Novel coronavirus structure data

+Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+Jul 12, 2017. Major update of PDB

-Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi