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- PDB-3qph: The three-dimensional structure of TrmB, a global transcriptional... -

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Basic information

Entry
Database: PDB / ID: 3qph
TitleThe three-dimensional structure of TrmB, a global transcriptional regulator of the hyperthermophilic archaeon Pyrococcus furiosus in complex with sucrose
ComponentsTrmB, a global transcription regulator
KeywordsTRANSCRIPTION / Transcriptional regulator
Function / homology
Function and homology information


SH3 type barrels. - #690 / Transcription regulator TrmB, C-terminal / Archaeal transcriptional regulator TrmB / Transcription regulator TrmB, N-terminal / Sugar-specific transcriptional regulator TrmB / Endonuclease Chain A / Endonuclease; Chain A / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / SH3 type barrels. / Arc Repressor Mutant, subunit A ...SH3 type barrels. - #690 / Transcription regulator TrmB, C-terminal / Archaeal transcriptional regulator TrmB / Transcription regulator TrmB, N-terminal / Sugar-specific transcriptional regulator TrmB / Endonuclease Chain A / Endonuclease; Chain A / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / SH3 type barrels. / Arc Repressor Mutant, subunit A / Winged helix DNA-binding domain superfamily / Roll / Winged helix-like DNA-binding domain superfamily / 2-Layer Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
sucrose / ACETATE ION / HTH-type sugar sensing transcriptional regulator TrmB
Similarity search - Component
Biological speciesPyrococcus furiosus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.992 Å
AuthorsKrug, M. / Lee, S.-J. / Boos, W. / Welte, W. / Diederichs, K.
CitationJournal: Protein Sci. / Year: 2013
Title: The three-dimensional structure of TrmB, a transcriptional regulator of dual function in the hyperthermophilic archaeon Pyrococcus furiosus in complex with sucrose.
Authors: Krug, M. / Lee, S.J. / Boos, W. / Diederichs, K. / Welte, W.
History
DepositionFeb 13, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 30, 2012Provider: repository / Type: Initial release
Revision 1.1Aug 28, 2013Group: Database references
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / entity_name_com / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_molecule_features / pdbx_nonpoly_scheme / pdbx_validate_close_contact / struct_asym / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.pdbx_synonyms / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.src_method / _entity.type / _struct_asym.entity_id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Feb 21, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2
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: TrmB, a global transcription regulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,63113
Polymers39,3421
Non-polymers1,28912
Water905
1
A: TrmB, a global transcription regulator
hetero molecules

A: TrmB, a global transcription regulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,26326
Polymers78,6842
Non-polymers2,57824
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555-x,-x+y,-z+2/31
Buried area12440 Å2
ΔGint-36 kcal/mol
Surface area32710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)158.522, 158.522, 79.153
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein TrmB, a global transcription regulator


Mass: 39342.035 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus furiosus (archaea) / Gene: PF1743 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9HGZ9
#2: Polysaccharide beta-D-fructofuranose-(2-1)-alpha-D-glucopyranose / sucrose


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 342.297 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: oligosaccharide with reducing-end-to-reducing-end glycosidic bond
References: sucrose
DescriptorTypeProgram
DFrufb2-1DGlcpaGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[ha122h-2b_2-5][a2122h-1a_1-5]/1-2/a2-b1WURCSPDB2Glycan 1.1.0
[][b-D-Fruf]{[(2+1)][a-D-Glcp]{}}LINUCSPDB-CARE
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 5 / 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: 8.54 Å3/Da / Density % sol: 85.61 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop / pH: 9
Details: 0.1 M BICINE, pH 9.0, 0.65 M NH4SO4, VAPOR DIFFUSION, HANGING DROP, temperature 296.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1.016 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: May 16, 2008
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.016 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. all: 28297 / Num. obs: 28240 / % possible obs: 99.8 % / Observed criterion σ(F): 1.1 / Observed criterion σ(I): 1.1

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
PHENIX(phenix.refine: 1.5_2)refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.992→43.396 Å / SU ML: 0.4 / σ(F): 1.99 / Phase error: 29.57 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2609 1997 8.6 %
Rwork0.2261 --
obs0.2292 23214 99.21 %
all-25977 -
Solvent computationShrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 102.684 Å2 / ksol: 0.342 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-12.1651 Å2-0 Å2-0 Å2
2--12.1651 Å2-0 Å2
3----24.3301 Å2
Refinement stepCycle: LAST / Resolution: 2.992→43.396 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2719 0 85 5 2809
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.012851
X-RAY DIFFRACTIONf_angle_d1.3853832
X-RAY DIFFRACTIONf_dihedral_angle_d16.7181070
X-RAY DIFFRACTIONf_chiral_restr0.082428
X-RAY DIFFRACTIONf_plane_restr0.005475
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9922-3.06710.4051360.37141410X-RAY DIFFRACTION93
3.0671-3.150.33341450.32111508X-RAY DIFFRACTION100
3.15-3.24260.31771360.27181499X-RAY DIFFRACTION100
3.2426-3.34720.27391460.2591499X-RAY DIFFRACTION99
3.3472-3.46680.41031430.31791473X-RAY DIFFRACTION99
3.4668-3.60560.27261420.24191535X-RAY DIFFRACTION100
3.6056-3.76960.29451390.24381528X-RAY DIFFRACTION100
3.7696-3.96820.32771350.25961490X-RAY DIFFRACTION99
3.9682-4.21660.23431480.21481522X-RAY DIFFRACTION100
4.2166-4.54190.21661430.1861530X-RAY DIFFRACTION100
4.5419-4.99830.20231480.17641508X-RAY DIFFRACTION100
4.9983-5.72020.23841420.21351556X-RAY DIFFRACTION100
5.7202-7.20150.31681490.25451555X-RAY DIFFRACTION100
7.2015-43.40070.23211450.20781604X-RAY DIFFRACTION100
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)
14.448-2.3109-2.4481.46820.6473.93281.5124-0.5399-1.0358-0.1586-1.81550.63711.5858-0.8547-0.46040.9861-0.12640.19770.2794-0.28360.776547.182-103.694720.6616
20.7956-0.09040.54110.35960.24521.6056-0.13760.3059-1.1251-0.0562-0.3408-0.93160.48590.11010.39911.20790.00270.34970.71130.14891.77343.1028-109.705232.4015
32.17032.4813-0.04814.0393-1.83250.7438-0.047-0.3775-0.4650.26250.0154-0.18-0.1015-0.09730.02171.11170.00490.17861.2634-0.00551.39752.3695-91.576334.1436
42.71840.50730.6145.22370.81371.6783-0.1214-0.2718-0.29430.1282-0.19190.56490.0579-0.49410.2120.12660.02290.07190.438-0.00170.271955.6444-64.073716.7917
54.68351.62421.33426.17965.57358.1648-0.4527-0.66641.1687-0.5687-0.69380.35180.446-0.66610.83882.3204-0.35020.08062.1889-0.58761.805550.0677-75.87133.7005
63.97132.33130.10532.021-0.31841.7941-0.190.06490.3144-0.23730.04690.2179-0.614-0.13730.2240.48490.0832-0.02190.38450.02370.128570.7362-51.537115.7341
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 8:21)
2X-RAY DIFFRACTION2(chain A and resid 22:51)
3X-RAY DIFFRACTION3(chain A and resid 52:107)
4X-RAY DIFFRACTION4(chain A and resid 108:203)
5X-RAY DIFFRACTION5(chain A and resid 204:214)
6X-RAY DIFFRACTION6(chain A and resid 215:342)

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