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- PDB-2ogg: Structure of B. subtilis trehalose repressor (TreR) effector bind... -

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Basic information

Entry
Database: PDB / ID: 2ogg
TitleStructure of B. subtilis trehalose repressor (TreR) effector binding domain
ComponentsTrehalose operon transcriptional repressor
KeywordsTRANSCRIPTION / gene repressor / sugar binding / Structural Genomics / PSI-2 / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG
Function / homology
Function and homology information


DNA-binding transcription factor activity / DNA binding
Similarity search - Function
Trehalose operon transcriptional repressor / UTRA / UbiC transcription regulator-associated / UTRA domain / Chorismate lyase / Chorismate lyase-like / Chorismate pyruvate-lyase/UbiC transcription regulator-associated domain superfamily / GntR-type HTH domain profile. / helix_turn_helix gluconate operon transcriptional repressor / Transcription regulator HTH, GntR ...Trehalose operon transcriptional repressor / UTRA / UbiC transcription regulator-associated / UTRA domain / Chorismate lyase / Chorismate lyase-like / Chorismate pyruvate-lyase/UbiC transcription regulator-associated domain superfamily / GntR-type HTH domain profile. / helix_turn_helix gluconate operon transcriptional repressor / Transcription regulator HTH, GntR / Bacterial regulatory proteins, gntR family / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
HTH-type transcriptional regulator TreR
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.5 Å
AuthorsRezacova, P. / Krejcirikova, V. / Borek, D. / Moy, S.F. / Joachimiak, A. / Otwinowski, Z. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: Proteins / Year: 2007
Title: The crystal structure of the effector-binding domain of the trehalose repressor TreR from Bacillus subtilis 168 reveals a unique quarternary assembly.
Authors: Rezacova, P. / Krejcirikova, V. / Borek, D. / Moy, S.F. / Joachimiak, A. / Otwinowski, Z.
History
DepositionJan 5, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 6, 2007Provider: repository / Type: Initial release
Revision 1.1Oct 15, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Derived calculations / Version format compliance
Revision 1.3Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_conn_type / 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 / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _struct_conn_type.id / _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

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Assembly

Deposited unit
A: Trehalose operon transcriptional repressor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,5367
Polymers18,0441
Non-polymers4916
Water64936
1
A: Trehalose operon transcriptional repressor
hetero molecules

A: Trehalose operon transcriptional repressor
hetero molecules

A: Trehalose operon transcriptional repressor
hetero molecules

A: Trehalose operon transcriptional repressor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,14228
Polymers72,1774
Non-polymers1,96624
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555-y,-x,-z1
crystal symmetry operation10_555-x,-y,z1
crystal symmetry operation15_555y,x,-z1
Buried area14210 Å2
ΔGint-176 kcal/mol
Surface area26270 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)69.719, 69.719, 236.535
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number98
Space group name H-MI4122
Components on special symmetry positions
IDModelComponents
11A-301-

NA

Detailsthe biological assembly is a dimer generated by the two fold axis: x, y, -z

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Components

#1: Protein Trehalose operon transcriptional repressor


Mass: 18044.209 Da / Num. of mol.: 1 / Fragment: Effector binding domain, residues 90-238
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Strain: 168 / Gene: treR / Plasmid: pMCSG7 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P39796
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 36 / 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: 3.98 Å3/Da / Density % sol: 69.11 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6
Details: Reservoir: 0.1M MES pH 6.0, 1.26M Ammonium sulfate, 0.56mM CYMAL-5. Protein: 21.2mg/ml. Drops: 1+1 microliter, 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: MARRESEARCH / Detector: CCD / Date: Oct 6, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. obs: 10126 / % possible obs: 95.6 % / Redundancy: 6 % / Biso Wilson estimate: 58.7 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 50
Reflection shellResolution: 2.5→2.54 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.278 / Mean I/σ(I) obs: 3.2 / % possible all: 70.5

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
HKL-3000data collection
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing
RefinementMethod to determine structure: SAD / Resolution: 2.5→37.88 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.918 / SU B: 15.803 / SU ML: 0.171 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.282 / ESU R Free: 0.242 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.24659 990 9.8 %RANDOM
Rwork0.19024 ---
all0.19576 10126 --
obs0.19576 10126 95.64 %-
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: 43.687 Å2
Baniso -1Baniso -2Baniso -3
1--0.71 Å20 Å20 Å2
2---0.71 Å20 Å2
3---1.42 Å2
Refinement stepCycle: LAST / Resolution: 2.5→37.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1213 0 29 36 1278
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0221262
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4121.9751697
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9385143
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.33723.33369
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.08215229
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.9261512
X-RAY DIFFRACTIONr_chiral_restr0.3580.2179
X-RAY DIFFRACTIONr_gen_planes_refined0.0250.02950
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2810.2456
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3370.2820
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1590.257
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2640.244
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1730.27
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.281.5718
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it3.7321168
X-RAY DIFFRACTIONr_scbond_it7.0273556
X-RAY DIFFRACTIONr_scangle_it9.324.5529
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.5→2.565 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.331 40 -
Rwork0.306 505 -
obs--70.87 %
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)
116.9599-3.032-0.986417.92616.702224.2622-0.7133-0.3265-0.16951.3141.3177-2.74510.69881.3356-0.6043-0.0779-0.06650.06160.1466-0.21410.191415.73513.17922.269
28.85650.15481.22469.67744.25911.6085-0.01170.40910.7664-1.0629-0.03120.9688-0.7731-0.69280.04290.13840.0343-0.06-0.070.01580.1119-4.14123.43417.563
315.6388-2.2105-7.78683.81681.93837.6348-0.2442-0.3247-0.18740.26010.4508-0.7460.02261.0925-0.2065-0.08390.0103-0.07290.0714-0.12190.066814.12414.90917.976
437.166110.0401-14.980418.0462-4.236722.83670.41890.55010.0730.4949-0.39071.4410.4026-0.5891-0.0282-0.1207-0.0825-0.0773-0.2064-0.0591-0.0471-4.30815.35820.075
50.76310.9799-2.06038.55694.482412.52370.135-0.0857-0.22150.04870.1422-0.62050.42620.2716-0.27720.00780.0675-0.0639-0.1139-0.08320.03343.9268.39925.073
622.35137.2604-1.74496.0338-6.28849.0432-0.3839-0.36310.00870.14760.2219-0.01380.1696-1.06650.1620.03680.002-0.0456-0.1157-0.01870.0278-4.9753.22518.257
738.107223.2219-11.992818.2896-7.745512.90660.29220.94831.04710.06360.57440.5985-0.5238-0.277-0.86660.2044-0.0120.037-0.117-0.0248-0.03254.51514.8513.964
823.897-0.35574.194322.8707-5.948112.9772-0.4335-0.00351.32260.470.6611-1.7836-1.39182.2541-0.22760.3492-0.38850.14240.3839-0.31570.310219.40723.65513.55
914.38682.1413-4.03415.2488-0.03086.36220.3067-0.10420.1237-0.31970.1942-0.0008-0.49720.2381-0.50090.0853-0.098-0.0347-0.0826-0.0631-0.16254.02714.9537.632
106.9781-2.9373-3.73734.19742.24193.92090.023-0.39630.0376-0.51020.448-0.3565-0.28350.8131-0.4710.0023-0.1530.03330.0633-0.0782-0.002210.36713.3628.704
1128.830111.212747.89924.360918.629179.5811-1.9058-5.31521.6729-0.2725-0.51982.2662-1.201-7.63542.42561.01510.7626-0.09711.6275-0.28620.77033.594-2.456-5.071
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA95 - 1019 - 15
2X-RAY DIFFRACTION2AA102 - 12316 - 37
3X-RAY DIFFRACTION3AA124 - 14138 - 55
4X-RAY DIFFRACTION4AA142 - 14856 - 62
5X-RAY DIFFRACTION5AA149 - 16463 - 78
6X-RAY DIFFRACTION6AA165 - 17379 - 87
7X-RAY DIFFRACTION7AA174 - 18588 - 99
8X-RAY DIFFRACTION8AA186 - 196100 - 110
9X-RAY DIFFRACTION9AA197 - 214111 - 128
10X-RAY DIFFRACTION10AA215 - 230129 - 144
11X-RAY DIFFRACTION11AA231 - 238145 - 152

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