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

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Basic information

Entry
Database: PDB / ID: 3bxg
TitleCrystal structure of effector binding domain of central glycolytic gene regulator (CggR) from Bacillus subtilis in complex with glucose-6-phosphate
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


carbohydrate binding / DNA 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 / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
6-O-phosphono-beta-D-glucopyranose / Central glycolytic genes regulator
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 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 / Refinement description / 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 / struct_ncs_dom_lim
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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)55,6414
Polymers55,1212
Non-polymers5202
Water8,773487
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.494, 83.806, 113.583
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Refine code: 4

Dom-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1GLYGLYASPASPAA93 - 3398 - 254
2LYSLYSARGARGBB89 - 3384 - 253

NCS ensembles : (Details: A B)
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-BG6 / 6-O-phosphono-beta-D-glucopyranose / BETA-D-GLUCOSE-6-PHOSPHATE / 6-O-phosphono-beta-D-glucose / 6-O-phosphono-D-glucose / 6-O-phosphono-glucose


Type: D-saccharide, beta linking / Mass: 260.136 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C6H13O9P
IdentifierTypeProgram
b-D-Glcp6PO3IUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 487 / 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: 2.4 Å3/Da / Density % sol: 48.66 %
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 10mM glucose-6-phosphate, 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: Oct 20, 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: 1.8→49.8 Å / Num. obs: 49657 / % possible obs: 99 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 6.7 % / Biso Wilson estimate: 25.5 Å2 / Rsym value: 0.075 / Net I/σ(I): 24.1
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.489 / Mean I/σ(I) obs: 1.9 / % possible all: 90.9

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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: 1.8→46.27 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.919 / SU B: 5.236 / SU ML: 0.092 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.129 / ESU R Free: 0.132 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23281 2507 5.1 %RANDOM
Rwork0.18 ---
obs0.18266 46775 98.85 %-
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: 26.798 Å2
Baniso -1Baniso -2Baniso -3
1--0.14 Å20 Å20 Å2
2---0.3 Å20 Å2
3---0.44 Å2
Refinement stepCycle: LAST / Resolution: 1.8→46.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3777 0 32 487 4296
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0224030
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4471.9825475
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.645552
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.31625.394165
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.82115754
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.9781521
X-RAY DIFFRACTIONr_chiral_restr0.0980.2639
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022973
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2110.22018
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3010.22805
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1610.2439
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2230.279
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.160.234
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.691.52664
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.01224153
X-RAY DIFFRACTIONr_scbond_it1.91931518
X-RAY DIFFRACTIONr_scangle_it3.0684.51299
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Ens-ID: 1 / Number: 1147 / Refine-ID: X-RAY DIFFRACTION

Auth asym-IDTypeRms dev position (Å)Weight position
Amedium positional0.690.5
Bmedium thermal1.092
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.32 185 -
Rwork0.252 3005 -
obs--87.76 %
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)
13.04020.58820.40495.15732.85964.71180.0319-0.2527-0.2480.1137-0.0389-0.07180.1405-0.03430.007-0.1464-0.0033-0.0135-0.11520.0443-0.139970.547474.363276.7147
26.4186-5.1109-2.18916.42571.38653.0795-0.1155-0.20330.03030.20550.21780.16570.0789-0.2464-0.1023-0.1273-0.0156-0.0079-0.08780.0121-0.16655.104578.055973.3615
32.5936-1.2792-0.16843.5456-0.032.26590.02180.2049-0.2709-0.10650.05490.22150.2238-0.2161-0.0766-0.0811-0.0165-0.0381-0.1089-0.0093-0.156957.917477.312664.4515
45.04660.7913-0.15863.2681-0.68063.9651-0.0240.3317-0.0934-0.15820.06880.1457-0.0576-0.0435-0.0449-0.07910.0057-0.0407-0.09560.0049-0.167455.754582.824959.8735
52.58917.5895-5.476325.3016-20.14817.0738-0.6732-0.5836-0.4318-0.8781-0.5637-2.3494-0.10521.37711.23690.219-0.0116-0.01190.24960.12920.351960.075898.795549.7082
63.0751-1.80970.9213.7474-1.06113.831-0.14930.15690.4145-0.06720.06440.2417-0.6224-0.29120.0849-0.01350.0168-0.051-0.09980.0178-0.070854.703793.957963.034
710.03510.6271-9.089711.9924-8.226510.9234-0.57120.5556-0.1312-1.09230.4422-0.43170.4318-0.30910.129-0.01-0.05810.0558-0.0051-0.0175-0.093278.26889.004256.8468
85.94240.8646-0.49574.71-1.65334.874-0.16520.31360.1222-0.17910.0631-0.1541-0.47350.26730.1021-0.0525-0.0701-0.0092-0.08150.015-0.141377.601892.827765.6416
93.2437-0.0410.57662.6104-0.05721.9311-0.05580.03630.26630.0451-0.0044-0.0082-0.25790.12960.0602-0.1161-0.0425-0.0026-0.11280.0027-0.180269.447586.650471.3647
1024.3892-0.029317.239622.39533.743624.54480.44220.1209-0.60230.64130.1528-1.13860.5997-0.2378-0.595-0.1209-0.0074-0.0286-0.07310.0041-0.117181.36374.259278.3475
112.59410.9867-0.66272.5032-0.52191.9477-0.0754-0.0762-0.22130.00740.0186-0.18110.12790.0790.0568-0.12170.0001-0.0197-0.1392-0.0028-0.132648.624574.263537.6639
127.2375-3.8873-2.78475.6643.6775.15430.0022-0.3558-0.01340.32660.068-0.217-0.0130.0011-0.0702-0.0742-0.0269-0.04-0.06040.0124-0.163452.450681.484144.7413
134.917-9.0476-3.922118.20368.434.07440.06760.16370.13540.23390.01620.1332-0.3661-0.3742-0.08380.19960.05720.0104-0.0047-0.0002-0.045953.1623100.885242.4641
144.24980.4828-1.31462.20490.27531.65110.0103-0.01670.2299-0.08350.0929-0.2806-0.18620.1002-0.1032-0.0960.0150.0166-0.13940.0048-0.152551.468788.320733.6126
155.8618-4.9596-1.206415.30024.33547.7292-0.071-0.24970.50371.2630.2965-0.4485-0.34650.4497-0.22560.15730.01750.1005-0.0416-0.0077-0.060832.88693.950747.8638
166.4457-0.03930.2595.7344-0.984.6971-0.0177-0.0080.21080.24210.14180.1684-0.4641-0.1743-0.1242-0.05850.04790.033-0.12060.0224-0.115830.978892.166137.8756
176.06981.7991.097714.348315.69320.43870.16210.23390.5854-0.4428-0.24510.1582-0.864-0.54050.083-0.080.01460.0217-0.07620.0543-0.046843.268192.906631.8642
182.22730.6184-0.53472.6832-1.21692.6385-0.00190.1182-0.066-0.0290.0520.2332-0.0544-0.1818-0.0502-0.13370.00140.0035-0.1282-0.0052-0.139733.754178.56134.0282
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A93 - 126
2X-RAY DIFFRACTION2A127 - 143
3X-RAY DIFFRACTION3A144 - 164
4X-RAY DIFFRACTION4A165 - 202
5X-RAY DIFFRACTION5A203 - 220
6X-RAY DIFFRACTION6A221 - 240
7X-RAY DIFFRACTION7A241 - 260
8X-RAY DIFFRACTION8A261 - 285
9X-RAY DIFFRACTION9A286 - 333
10X-RAY DIFFRACTION10A334 - 339
11X-RAY DIFFRACTION11B120 - 178
12X-RAY DIFFRACTION12B179 - 202
13X-RAY DIFFRACTION13B203 - 221
14X-RAY DIFFRACTION14B222 - 242
15X-RAY DIFFRACTION15B243 - 260
16X-RAY DIFFRACTION16B261 - 285
17X-RAY DIFFRACTION17B286 - 296
18X-RAY DIFFRACTION18B297 - 332

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