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

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Basic information

Entry
Database: PDB / ID: 3bxf
TitleCrystal structure of effector binding domain of central glycolytic gene regulator (CggR) from Bacillus subtilis in complex with effector fructose-1,6-bisphosphate
ComponentsCentral glycolytic gene regulator
KeywordsGENE 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
: / CggR N-terminal DNA binding domain / Sugar-binding domain, putative / : / Putative sugar-binding domain / Rossmann fold - #1360 / NagB/RpiA transferase-like / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / Rossmann fold ...: / CggR N-terminal DNA binding domain / Sugar-binding domain, putative / : / Putative sugar-binding domain / Rossmann fold - #1360 / NagB/RpiA transferase-like / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
1,3-DIHYDROXYACETONEPHOSPHATE / 1,6-di-O-phosphono-beta-D-fructofuranose / Central glycolytic genes regulator
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsRezacova, P. / Otwinowski, Z.
CitationJournal: 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
DepositionJan 13, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 1, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Jul 29, 2020Group: 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 1.3Aug 30, 2023Group: 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Central glycolytic gene regulator
B: Central glycolytic gene regulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,7738
Polymers55,1212
Non-polymers6526
Water11,440635
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.447, 83.245, 116.457
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsAUTHORS STATE THAT THE DIMERIC ASSEMBLY OF THE BIOLOGICAL UNIT THAT IS SHOWN IN REMARK 350 IS PUTATIVE AT THE TIME OF DEPOSITION.

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Components

#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-FBP / 1,6-di-O-phosphono-beta-D-fructofuranose / BETA-FRUCTOSE-1,6-DIPHOSPHATE / FRUCTOSE-1,6-BISPHOSPHATE / 1,6-di-O-phosphono-beta-D-fructose / 1,6-di-O-phosphono-D-fructose / 1,6-di-O-phosphono-fructose


Type: D-saccharide, beta linking / Mass: 340.116 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C6H14O12P2
IdentifierTypeProgram
b-D-Fruf1PO36PO3IUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-13P / 1,3-DIHYDROXYACETONEPHOSPHATE


Mass: 170.058 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H7O6P
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 635 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.26 Å3/Da / Density % sol: 45.62 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.6
Details: Reservoir: 0.2M Ammonium formate pH 6.6, 20% (w/v) PEG 3350. 25mg/ml protein with 90mM fructose-1,6-bisphosphate, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.979 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Dec 11, 2007
RadiationMonochromator: Rosenbaum-Rock high-resolution double crystal Si(111)
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.7→23.94 Å / Num. obs: 50944 / % possible obs: 91.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 4.7 % / Biso Wilson estimate: 29 Å2 / Rmerge(I) obs: 0.073 / Net I/σ(I): 21.86
Reflection shellResolution: 1.7→1.76 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.66 / Mean I/σ(I) obs: 2 / % possible all: 94.2

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Processing

Software
NameVersionClassification
REFMAC5.3.0037refinement
HKL-3000data collection
HKL-3000data reduction
HKL-3000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2OKG

2okg


Resolution: 1.7→22.64 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.909 / SU B: 6.006 / SU ML: 0.106 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.13 / ESU R Free: 0.134 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25678 2727 5.1 %RANDOM
Rwork0.20067 ---
obs0.2035 50942 96.33 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 31.484 Å2
Baniso -1Baniso -2Baniso -3
1-0.46 Å20 Å20 Å2
2---0.54 Å20 Å2
3---0.08 Å2
Refinement stepCycle: LAST / Resolution: 1.7→22.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3765 0 34 635 4434
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0223933
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3981.9845325
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4915523
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.65225.032157
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.94515736
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.2681523
X-RAY DIFFRACTIONr_chiral_restr0.0940.2619
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022875
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2140.22082
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.30.22755
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.160.2538
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2070.258
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1510.232
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.6181.52601
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.924057
X-RAY DIFFRACTIONr_scbond_it1.73831477
X-RAY DIFFRACTIONr_scangle_it2.5994.51258
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.7→1.745 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.331 186 -
Rwork0.277 3513 -
obs--91.06 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°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)
13.32014.06472.336920.5224.709112.702-0.4278-0.3250.67580.2874-0.2060.67160.9339-0.61110.63380.0151-0.02270.0278-0.0525-0.0227-0.037512.778-21.45227.35
21.19340.99290.33622.18521.24824.11370.0555-0.1265-0.04880.099-0.0756-0.23320.0647-0.00410.0202-0.13510.0427-0.0007-0.12610.0338-0.108615.747-10.82720.145
33.3473-0.9085-1.44771.9858-0.79592.5649-0.07720.1229-0.23380.00370.04590.12650.1658-0.24520.0313-0.1606-0.02490.0121-0.1557-0.008-0.16161.933-7.6212.276
424.05252.3516-12.92113.32551.498210.03030.1905-0.1348-0.00340.6907-0.01490.04560.3667-0.3958-0.17560.005-0.07080.0269-0.04960.0466-0.0727-6.995-11.99913.382
52.88431.4929-1.76194.7526-2.81575.8572-0.10050.33090.0202-0.01940.0833-0.1782-0.149-0.27950.0171-0.16040.00570.0036-0.10370.0415-0.1699-1.2892.116.066
663.18251.6918-53.584112.151-17.372866.42740.29380.76841.9281-0.9366-0.3019-0.12561.65031.50120.00820.03570.035-0.00590.18190.0923-0.11289.3034.682-7.869
71.3892.2141-1.42794.8002-4.32486.7087-0.07760.0689-0.029-0.26150.13420.10370.4335-0.1789-0.0566-0.1088-0.0135-0.0033-0.09860.0138-0.1568-1.719-1.7690.6
86.1513-0.5988-4.49372.1288-1.14919.3913-0.1748-0.3083-0.08450.39880.1909-0.259-0.30490.1222-0.0161-0.04650.0198-0.0385-0.1442-0.039-0.07232.22817.529-5.913
92.5778-0.00550.15440.06970.06421.6887-0.17040.0970.12460.09260.1091-0.0018-0.3138-0.22510.0613-0.12150.02180.024-0.14820.0091-0.1150.2176.6238.267
107.6416-5.00163.04217.8489-11.868143.11670.19440.5194-1.0406-0.39040.17130.1184-0.09491.7572-0.3658-0.1755-0.02890.023-0.0731-0.0851-0.014622.2310.4962.331
113.42080.3281-1.57032.9494-0.15742.70960.09420.3076-0.1382-0.1748-0.0642-0.0625-0.31470.0646-0.0299-0.1241-0.0196-0.005-0.12160.0006-0.164220.8198.4264.92
124.4364-0.225-1.77960.2697-1.28988.0879-0.05430.08250.39980.10180.06760.1801-0.3205-0.0056-0.0133-0.00050.0086-0.0128-0.13120.033-0.04827.81411.487.638
1312.8961-5.327-3.01632.65070.14693.3883-0.0489-0.19890.09670.39270.0684-0.0837-0.2132-0.1262-0.0195-0.1320.00890.0373-0.16750.0112-0.18136.6960.09616.473
143.12490.4929-0.94525.0632-0.37612.69630.1111-0.1271-0.08940.2587-0.2158-0.3524-0.16470.27060.1047-0.1464-0.011-0.0281-0.14610.0301-0.170217.436-2.517.26
158.14411.222510.009423.54315.481920.85320.1586-0.2798-0.70880.94230.006-2.97681.0281.0168-0.1647-0.06220.0587-0.0890.05560.12890.216325.167-10.15920.691
1610.168-8.916613.085710.729-11.039916.90580.266-0.0483-0.8321-0.913-0.01070.72050.9601-0.5457-0.25530.03840.0099-0.11890.0374-0.19160.2028-24.011-15.275-29.651
173.3619-1.75511.00813.9179-3.0639.42160.11740.1002-0.818-0.2225-0.18390.4569-0.0367-0.14470.0665-0.1045-0.0157-0.1025-0.1409-0.03650.138-21.406-11.327-22.905
181.9222.048-1.20863.6416-2.16362.73670.08760.0958-0.3809-0.24120.04540.15740.23290.0476-0.133-0.12780.0294-0.0682-0.1418-0.02650.0115-6.944-10.545-21.451
193.8945-0.7047-0.08275.7418-0.123.71430.1417-0.2323-0.6583-0.13150.01570.01260.31220.1629-0.1574-0.1406-0.0231-0.0712-0.13980.0648-0.0194-5.635-8.605-15.221
2012.4053-6.8909-3.333511.12913.7336.70010.07840.3878-1.1967-0.1698-0.22430.40190.81770.41740.1459-0.05140.0565-0.0462-0.0563-0.0317-0.04043.176-6.08-24.106
215.1266-0.55674.21738.5042-4.74047.77990.0408-0.28790.0838-0.0494-0.2594-0.0134-0.27270.06410.2186-0.1319-0.01480.0008-0.06070.0073-0.1812-9.255.721-9.766
222.9629-0.432-0.1895.18142.16133.05810.1779-0.2002-0.3743-0.0649-0.0889-0.27760.00870.1381-0.089-0.1673-0.0103-0.0213-0.10560.0511-0.14811.051-0.68-14.148
230.3126-1.2345-1.09635.39454.23013.8649-0.10280.26770.1413-0.0784-0.14510.2763-0.1709-0.28140.2479-0.10630.00420.0192-0.1055-0.0137-0.0687-0.39116.447-17.699
245.6037-1.136-2.15652.14310.36684.39240.0309-0.3056-0.31340.09860.03770.2788-0.1111-0.0918-0.0686-0.16030.0091-0.0222-0.13340.0315-0.1517-15.1442.162-16.287
2535.01870.77314.95331.37983.158526.1687-0.5015-1.47381.0584-0.03790.50280.1452-1.8197-0.3131-0.00130.17370.11720.0411-0.0128-0.0784-0.0145-23.09615.558-9.977
266.0637-0.4459-0.45235.3045-0.41283.1694-0.107-0.14840.11320.10110.11970.2427-0.3199-0.2962-0.0127-0.13640.0401-0.0334-0.12880.0027-0.1394-22.668.568-20.353
2736.98774.4908-3.080710.926610.020310.664-0.7338-0.24140.2262-0.76740.9132-0.4286-0.27830.553-0.1794-0.04690.00490.0169-0.0685-0.0280.0033-10.69414.472-18.31
2829.7659-4.7742-0.52081.76223.16549.5403-0.30660.86440.9128-0.38740.06780.4313-0.55210.26520.2387-0.0576-0.0146-0.0529-0.12220.0123-0.0614-10.6619.653-26.928
294.0385-0.4325-0.14731.0442-0.48712.43120.15180.1085-0.4493-0.11490.00120.1834-0.0003-0.1299-0.153-0.13840.0127-0.0678-0.1451-0.027-0.0575-18.727-3.223-24.609
3024.4687-11.520614.709812.5094-3.533527.75030.4087-0.6611-2.5968-0.15340.35421.81970.4229-1.2802-0.7629-0.1154-0.0671-0.0759-0.02160.07110.3763-29.913-11.087-20.73
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA86 - 931 - 8
2X-RAY DIFFRACTION2AA94 - 1249 - 39
3X-RAY DIFFRACTION3AA125 - 15840 - 73
4X-RAY DIFFRACTION4AA159 - 16674 - 81
5X-RAY DIFFRACTION5AA167 - 17982 - 94
6X-RAY DIFFRACTION6AA180 - 18495 - 99
7X-RAY DIFFRACTION7AA185 - 208100 - 123
8X-RAY DIFFRACTION8AA209 - 222124 - 137
9X-RAY DIFFRACTION9AA223 - 242138 - 157
10X-RAY DIFFRACTION10AA243 - 249158 - 164
11X-RAY DIFFRACTION11AA250 - 284165 - 199
12X-RAY DIFFRACTION12AA285 - 295200 - 210
13X-RAY DIFFRACTION13AA296 - 307211 - 222
14X-RAY DIFFRACTION14AA308 - 333223 - 248
15X-RAY DIFFRACTION15AA334 - 338249 - 253
16X-RAY DIFFRACTION16BB94 - 1029 - 17
17X-RAY DIFFRACTION17BB103 - 12018 - 35
18X-RAY DIFFRACTION18BB121 - 14736 - 62
19X-RAY DIFFRACTION19BB148 - 16363 - 78
20X-RAY DIFFRACTION20BB164 - 17479 - 89
21X-RAY DIFFRACTION21BB175 - 18490 - 99
22X-RAY DIFFRACTION22BB185 - 205100 - 120
23X-RAY DIFFRACTION23BB206 - 232121 - 147
24X-RAY DIFFRACTION24BB233 - 251148 - 166
25X-RAY DIFFRACTION25BB252 - 263167 - 178
26X-RAY DIFFRACTION26BB264 - 283179 - 198
27X-RAY DIFFRACTION27BB284 - 289199 - 204
28X-RAY DIFFRACTION28BB290 - 294205 - 209
29X-RAY DIFFRACTION29BB295 - 331210 - 246
30X-RAY DIFFRACTION30BB332 - 338247 - 253

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