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- PDB-4xxh: TREHALOSE REPRESSOR FROM ESCHERICHIA COLI -

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Basic information

Entry
Database: PDB / ID: 4xxh
TitleTREHALOSE REPRESSOR FROM ESCHERICHIA COLI
ComponentsHTH-type transcriptional regulator TreR
KeywordsGENE REGULATION / LACI FAMILY / PHOSPHATE BINDING / PROTEIN STRUCTURE / TREHALOSE REPRESSOR
Function / homology
Function and homology information


trehalose metabolic process / transcription cis-regulatory region binding / DNA-binding transcription factor activity / negative regulation of DNA-templated transcription / regulation of DNA-templated transcription
Similarity search - Function
Trehalose operon repressor / LacI-type HTH domain signature. / Periplasmic binding protein-like domain / LacI-type HTH domain / Bacterial regulatory proteins, lacI family / LacI-type HTH domain profile. / helix_turn _helix lactose operon repressor / Lambda repressor-like, DNA-binding domain superfamily / Response regulator / Periplasmic binding protein-like I ...Trehalose operon repressor / LacI-type HTH domain signature. / Periplasmic binding protein-like domain / LacI-type HTH domain / Bacterial regulatory proteins, lacI family / LacI-type HTH domain profile. / helix_turn _helix lactose operon repressor / Lambda repressor-like, DNA-binding domain superfamily / Response regulator / Periplasmic binding protein-like I / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
trehalose-6-phosphate / HTH-type transcriptional regulator TreR
Similarity search - Component
Biological speciesEscherichia coli K-12 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 2.4 Å
AuthorsHars, U. / Horlacher, R. / Boos, W. / Smart, O.S. / Bricogne, G. / Welte, W. / Diederichs, K.
Citation
Journal: PROTEIN SCI. / Year: 1998
Title: CRYSTAL STRUCTURE OF THE EFFECTOR-BINDING DOMAIN OF THE TREHALOSE-REPRESSOR OF ESCHERICHIA COLI, A MEMBER OF THE LACI FAMILY, IN ITS COMPLEXES WITH INDUCER TREHALOSE-6-PHOSPHATE AND NONINDUCER TREHALOSE.
Authors: Hars, U. / Horlacher, R. / Boos, W. / Welte, W. / Diederichs, K.
History
DepositionJan 30, 2015Deposition site: RCSB / Processing site: PDBE
SupersessionFeb 11, 2015ID: 1BYK
Revision 1.0Feb 11, 2015Provider: repository / Type: Initial release
Revision 1.1Jun 10, 2015Group: Non-polymer description
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / diffrn_radiation_wavelength / 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 / struct_conn / 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_atom_id / _atom_site.label_comp_id / _atom_site.occupancy / _atom_site.type_symbol / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_auth_comp_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_atom_id / _atom_site_anisotrop.pdbx_label_comp_id / _atom_site_anisotrop.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.src_method / _entity.type
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: HTH-type transcriptional regulator TreR
B: HTH-type transcriptional regulator TreR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,7754
Polymers55,9302
Non-polymers8452
Water1,42379
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4730 Å2
ΔGint-19 kcal/mol
Surface area19860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.890, 84.890, 169.000
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number170
Space group name H-MP65

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Components

#1: Protein HTH-type transcriptional regulator TreR / Trehalose operon repressor


Mass: 27965.197 Da / Num. of mol.: 2 / Fragment: EFFECTOR BINDING DOMAIN, UNP residues 61-315 / Source method: isolated from a natural source / Source: (natural) Escherichia coli K-12 (bacteria) / References: UniProt: P36673
#2: Polysaccharide 6-O-phosphono-alpha-D-glucopyranose-(1-1)-alpha-D-glucopyranose / trehalose-6-phosphate


Type: oligosaccharide, Oligosaccharide / Class: Substrate analog / Mass: 422.277 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: oligosaccharide with reducing-end-to-reducing-end glycosidic bond
References: trehalose-6-phosphate
DescriptorTypeProgram
WURCS=2.0/2,2,1/[a2122h-1a_1-5][a2122h-1a_1-5_6*OPO/3O/3=O]/1-2/a1-b1WURCSPDB2Glycan 1.1.0
[][a-D-Glcp]{[(1+1)][a-D-Glcp]{[(6+0)][P]{}}}LINUCSPDB-CARE
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 79 / 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: 2.7 Å3/Da / Density % sol: 54 %
Crystal growTemperature: 300 K / Method: vapor diffusion, hanging drop / pH: 5.5 / Details: 1.6-1.9M sodium formate, 0.1M sodium acetate / PH range: 5.2-5.5

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Data collection

DiffractionMean temperature: 277 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BL19 / Wavelength: 0.905 Å
DetectorType: CUSTOM-MADE / Detector: CCD / Date: Apr 15, 1996
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.905 Å / Relative weight: 1
ReflectionResolution: 2.4→40 Å / Num. obs: 25724 / % possible obs: 95.5 % / Observed criterion σ(I): 0 / Redundancy: 5.9 % / Biso Wilson estimate: 57.89 Å2 / Rsym value: 0.086 / Net I/σ(I): 14
Reflection shellResolution: 2.4→2.5 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.67 / Mean I/σ(I) obs: 1.5 / Rsym value: 0.334 / % possible all: 72.1

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Processing

Software
NameVersionClassification
PDB_EXTRACT3.11data extraction
XDSdata reduction
XSCALEdata scaling
BUSTER2.11.6refinement
DENZOdata reduction
DAREFIphasing
RefinementMethod to determine structure: MIR / Resolution: 2.4→36.76 Å / Cor.coef. Fo:Fc: 0.9687 / Cor.coef. Fo:Fc free: 0.9629 / Occupancy max: 1 / Occupancy min: 0 / SU R Cruickshank DPI: 0.233 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.218 / SU Rfree Blow DPI: 0.159 / SU Rfree Cruickshank DPI: 0.164
Details: This entry represents a re-refinement of PDB entry 1BYK using a new set of structure factors obtained by re-processing the original images. The stereochemistry for the trehalose-6-phosphate ...Details: This entry represents a re-refinement of PDB entry 1BYK using a new set of structure factors obtained by re-processing the original images. The stereochemistry for the trehalose-6-phosphate ligand has been corrected.
RfactorNum. reflection% reflectionSelection details
Rfree0.173 1278 4.97 %RANDOM
Rwork0.151 ---
obs0.1521 25714 95.53 %-
Displacement parametersBiso max: 127.28 Å2 / Biso mean: 56.8085 Å2 / Biso min: 31.82 Å2
Baniso -1Baniso -2Baniso -3
1--3.8329 Å20 Å20 Å2
2---3.8329 Å20 Å2
3---7.6658 Å2
Refine analyzeLuzzati coordinate error obs: 0.271 Å
Refinement stepCycle: LAST / Resolution: 2.4→36.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3805 0 54 79 3938
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d1328SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes85HARMONIC2
X-RAY DIFFRACTIONt_gen_planes576HARMONIC5
X-RAY DIFFRACTIONt_it3977HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion558SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact4546SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d3977HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg5474HARMONIC21.09
X-RAY DIFFRACTIONt_omega_torsion2.91
X-RAY DIFFRACTIONt_other_torsion17.66
LS refinement shellResolution: 2.4→2.5 Å / Total num. of bins used: 13
RfactorNum. reflection% reflection
Rfree0.2715 103 4.72 %
Rwork0.2288 2080 -
all0.2308 2183 -
obs--71.53 %
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)
11.8353-0.06480.08361.5063-0.06131.58840.03780.0289-0.1723-0.0040.0238-0.24580.22540.1837-0.0616-0.04390.0206-0.0145-0.1416-0.0229-0.103728.7552-11.656523.811
21.57180.4120.02831.5745-0.25271.81830.0107-0.05910.1440.1694-0.0086-0.1748-0.46810.1213-0.00210.0288-0.037-0.0287-0.1803-0.017-0.14526.446216.395626.8506
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A61 - 339
2X-RAY DIFFRACTION2{ B|* }B61 - 337

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