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

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Basic information

Entry
Database: PDB / ID: 3bxe
TitleCrystal structure of effector binding domain of central glycolytic gene regulator (CggR) from Bacillus subtilis in complex with dihydroxyacetone 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
1,3-DIHYDROXYACETONEPHOSPHATE / Central glycolytic genes regulator
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / 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 1.2Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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)55,4614
Polymers55,1212
Non-polymers3402
Water10,863603
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)55.537, 83.822, 113.712
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: Chemical ChemComp-13P / 1,3-DIHYDROXYACETONEPHOSPHATE / Dihydroxyacetone phosphate


Mass: 170.058 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H7O6P
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 603 / 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: 48.77 %
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 glyceraldehyde-3-phosphate, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E+ DW / Wavelength: 1.54178 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Mar 3, 2007
RadiationMonochromator: Ni / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 1.8→35.9 Å / Num. obs: 49172 / % possible obs: 99.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 4.9 % / Biso Wilson estimate: 33.1 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 38.7
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.51 / Mean I/σ(I) obs: 2.1 / % possible all: 95.6

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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→35.9 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.946 / SU B: 3.971 / SU ML: 0.084 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.128 / ESU R Free: 0.122 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.21538 2517 5.1 %RANDOM
Rwork0.17703 ---
obs0.17899 47018 99.02 %-
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: 31.328 Å2
Baniso -1Baniso -2Baniso -3
1-0.34 Å20 Å20 Å2
2---0.81 Å20 Å2
3---0.47 Å2
Refinement stepCycle: LAST / Resolution: 1.8→35.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3786 0 20 603 4409
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0223954
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2341.9795354
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.0285533
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.74425.427164
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.69915744
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.0411521
X-RAY DIFFRACTIONr_chiral_restr0.0840.2618
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022919
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1990.21946
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.2990.22747
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1490.2506
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1670.265
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1360.236
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.6441.52615
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.02824076
X-RAY DIFFRACTIONr_scbond_it1.92231484
X-RAY DIFFRACTIONr_scangle_it3.1394.51261
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.8→1.846 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.323 169 -
Rwork0.248 3185 -
obs--92.19 %
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)
18.22862.37130.348312.0257-0.56767.3393-0.1005-0.44630.56210.43030.1350.0021-0.5448-0.2161-0.0345-0.09530.02860.02120.0194-0.0457-0.1529-44.3048.83427.742
22.14570.16780.1513.8351-1.86843.84610.0014-0.01120.1773-0.0713-0.01860.1609-0.1156-0.00410.0172-0.15480.00830.0028-0.0941-0.0285-0.1467-42.87710.52715.923
31.667-0.1629-0.05361.80260.42892.0706-0.0578-0.01490.07340.00110.097-0.1701-0.03850.1426-0.0392-0.1238-0.01630.0137-0.0774-0.0004-0.1756-27.594.36311.013
47.83042.80361.59692.99251.05642.6246-0.13250.45810.0708-0.20280.1231-0.0841-0.08370.10460.0094-0.0712-0.00430.0287-0.02720.0061-0.1915-30.2441.6210.015
51.56743.18022.629.43934.84697.7612-0.0211-0.07430.05840.0496-0.11160.62440.4756-0.47190.13270.0443-0.03740.07220.0651-0.026-0.0231-30.819-15.416-6.616
62.33870.04010.30961.57650.19972.0992-0.11980.0368-0.1098-0.15520.09340.02920.2191-0.07370.0264-0.0784-0.0430.0155-0.11510.0088-0.1922-36.677-5.5635.99
71.95890.56212.44223.10141.3863.25570.00850.0893-0.0358-0.14230.00590.14850.2898-0.0746-0.0145-0.0732-0.0612-0.0055-0.0425-0.0056-0.1509-50.769-9.6215.598
82.34040.0016-0.25321.53950.04040.9127-0.13980.0895-0.2453-0.01970.0717-0.06720.1801-0.09340.0681-0.0909-0.02350.0172-0.0616-0.0126-0.1655-37.697-6.91411.335
93.1423-0.06390.13062.4667-0.5442.42750.0298-0.1090.00560.0942-0.02780.1330.0098-0.225-0.002-0.159-0.02270.0078-0.067-0.0073-0.2048-46.2272.02217.798
1018.2691-3.7512-7.242519.248410.727836.8360.0085-0.2020.6532-0.2270.01090.5317-0.996-0.2698-0.0193-0.11180.01670.0013-0.0393-0.0086-0.1133-54.3339.37622.493
111.2487-0.1983-0.41682.98310.75972.89550.02090.05360.0904-0.02950.0001-0.2-0.0060.0448-0.021-0.1201-0.00780.0076-0.0387-0.0188-0.1089-3.85414.789-21.839
121.86530.66870.50321.7402-0.05070.9898-0.02210.02790.14890.00640.01150.1454-0.02410.00210.0106-0.1504-0.00150.0086-0.10450.0094-0.1595-18.8910.269-19.762
131.9588-0.08490.28932.97720.48362.048-0.0024-0.03360.182-0.2166-0.04640.1884-0.1329-0.09920.0487-0.09820.00270.0245-0.08070.0177-0.119-26.2547.864-20.26
144.9148-2.7221.17045.0007-1.80252.43370.0021-0.1729-0.00020.2372-0.04580.2249-0.0063-0.12010.0437-0.086-0.02610.033-0.05110.0029-0.172-24.1011.681-11.977
152.3219-4.3450.901117.5743-4.49651.1860.07060.135-0.02050.0129-0.0528-0.11620.05410.188-0.01780.13050.04890.0270.07770.0102-0.0488-24.537-16.974-13.666
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A93 - 103
2X-RAY DIFFRACTION2A104 - 126
3X-RAY DIFFRACTION3A127 - 176
4X-RAY DIFFRACTION4A177 - 202
5X-RAY DIFFRACTION5A203 - 224
6X-RAY DIFFRACTION6A225 - 251
7X-RAY DIFFRACTION7A252 - 284
8X-RAY DIFFRACTION8A285 - 309
9X-RAY DIFFRACTION9A310 - 335
10X-RAY DIFFRACTION10A336 - 340
11X-RAY DIFFRACTION11B86 - 122
12X-RAY DIFFRACTION12B123 - 156
13X-RAY DIFFRACTION13B157 - 177
14X-RAY DIFFRACTION14B178 - 202
15X-RAY DIFFRACTION15B203 - 219

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