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- PDB-2jhe: N-terminal domain of TyrR transcription factor (residues 1 - 190) -

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Basic information

Entry
Database: PDB / ID: 2jhe
TitleN-terminal domain of TyrR transcription factor (residues 1 - 190)
ComponentsTRANSCRIPTION REGULATOR TYRR
KeywordsTRANSCRIPTION / AROMATIC HYDROCARBONS CATABOLISM / TYRR PROTEIN / NUCLEOTIDE-BINDING / TRANSCRIPTION REGULATION / ACTIVATOR / REPRESSOR / ATP-BINDING / DNA-BINDING / TWO-COMPONENT REGULATORY SYSTEM
Function / homology
Function and homology information


: / phosphorelay signal transduction system / transcription factor binding / negative regulation of DNA-templated transcription / regulation of DNA-templated transcription / DNA binding / ATP binding / cytosol
Similarity search - Function
TyrR family, helix-turn-helix domain / Helix-turn-helix domain / PAS domain / Sigma-54 interaction domain ATP-binding region A signature. / Sigma-54 interaction domain, conserved site / Sigma-54 interaction domain C-terminal part signature. / Sigma-54 interaction domain, ATP-binding site 2 / Sigma-54 interaction domain ATP-binding region B signature. / Sigma-54 interaction domain, ATP-binding site 1 / ACT domain ...TyrR family, helix-turn-helix domain / Helix-turn-helix domain / PAS domain / Sigma-54 interaction domain ATP-binding region A signature. / Sigma-54 interaction domain, conserved site / Sigma-54 interaction domain C-terminal part signature. / Sigma-54 interaction domain, ATP-binding site 2 / Sigma-54 interaction domain ATP-binding region B signature. / Sigma-54 interaction domain, ATP-binding site 1 / ACT domain / Sigma-54 interaction domain profile. / Sigma-54 interaction domain / RNA polymerase sigma factor 54 interaction domain / ACT domain profile. / ACT domain / PAS domain / Beta-Lactamase / PAS domain / PAS repeat profile. / PAS domain / PAS domain superfamily / Homeobox-like domain superfamily / Alpha-Beta Plaits / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
2-(2-ETHOXYETHOXY)ETHANOL / Transcriptional regulatory protein TyrR
Similarity search - Component
Biological speciesESCHERICHIA COLI (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 2.3 Å
AuthorsVerger, D. / Carr, P.D. / Kwok, T. / Ollis, D.L.
CitationJournal: J.Mol.Biol. / Year: 2007
Title: Crystal Structure of the N-Terminal Domain of the Tyrr Transcription Factor Responsible for Gene Regulation of Aromatic Amino Acid Biosynthesis and Transport in Escherichia Coli K12
Authors: Verger, D. / Carr, P.D. / Kwok, T. / Ollis, D.L.
History
DepositionFeb 21, 2007Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 24, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Refinement description / Version format compliance
Revision 1.2Jan 24, 2018Group: Source and taxonomy / Category: entity_src_gen
Item: _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_strain
Revision 1.3May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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: TRANSCRIPTION REGULATOR TYRR
B: TRANSCRIPTION REGULATOR TYRR
C: TRANSCRIPTION REGULATOR TYRR
D: TRANSCRIPTION REGULATOR TYRR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,5158
Polymers86,8964
Non-polymers6194
Water2,630146
1
A: TRANSCRIPTION REGULATOR TYRR
B: TRANSCRIPTION REGULATOR TYRR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,8725
Polymers43,4482
Non-polymers4243
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4430 Å2
ΔGint-38.4 kcal/mol
Surface area22840 Å2
MethodPQS
2
C: TRANSCRIPTION REGULATOR TYRR
D: TRANSCRIPTION REGULATOR TYRR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,6423
Polymers43,4482
Non-polymers1941
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4640 Å2
ΔGint-41.1 kcal/mol
Surface area21910 Å2
MethodPQS
Unit cell
Length a, b, c (Å)134.456, 72.009, 96.814
Angle α, β, γ (deg.)90.00, 98.46, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
TRANSCRIPTION REGULATOR TYRR


Mass: 21723.998 Da / Num. of mol.: 4 / Fragment: N-TERMINAL DOMAIN, RESIDUES 1-190
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Strain: K12 / Production host: ESCHERICHIA COLI K-12 (bacteria) / References: UniProt: P07604
#2: Chemical ChemComp-AE3 / 2-(2-ETHOXYETHOXY)ETHANOL


Mass: 134.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O3
#3: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 146 / Source method: isolated from a natural source / Formula: H2O
Compound detailsINVOLVED IN TRANSCRIPTIONAL REGULATION OF AROMATIC AMINO ACID BIOSYNTHESIS AND TRANSPORT. MODULATES ...INVOLVED IN TRANSCRIPTIONAL REGULATION OF AROMATIC AMINO ACID BIOSYNTHESIS AND TRANSPORT. MODULATES THE EXPRESSION OF AT LEAST 8 UNLINKED OPERONS. SEVEN OF THESE OPERONS ARE REGULATED IN RESPONSE TO CHANGES IN THE CONCENTRATION OF THE THREE AROMATIC AMINO ACIDS (PHENYLALANINE, TYROSINE AND TRYPTOPHAN).

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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: 2.5 Å3/Da / Density % sol: 50.3 % / Description: NONE
Crystal growpH: 6.3
Details: 0.31 M AMMONIUM SULFATE, 33% PEG-MME 5000, 0.1 M MES, PH 6.3

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.969
DetectorType: MARRESEARCH / Detector: CCD / Date: Dec 15, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.969 Å / Relative weight: 1
ReflectionResolution: 2.3→24.4 Å / Num. obs: 40199 / % possible obs: 98.2 % / Observed criterion σ(I): 0 / Redundancy: 12.8 % / Rmerge(I) obs: 0.04 / Net I/σ(I): 17.5
Reflection shellResolution: 2.3→2.36 Å / % possible all: 94.6

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: SIRAS
Starting model: NONE

Resolution: 2.3→24.4 Å / Cor.coef. Fo:Fc: 0.919 / Cor.coef. Fo:Fc free: 0.866 / SU B: 18.346 / SU ML: 0.244 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.373 / ESU R Free: 0.293 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.317 1967 4.9 %RANDOM
Rwork0.248 ---
obs0.252 38114 98.2 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 42.54 Å2
Baniso -1Baniso -2Baniso -3
1--2.15 Å20 Å2-1.14 Å2
2---0.65 Å20 Å2
3---2.46 Å2
Refinement stepCycle: LAST / Resolution: 2.3→24.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5716 0 38 146 5900
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0225846
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.8711.9737934
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.2415746
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.54523.566258
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.97815939
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.2191552
X-RAY DIFFRACTIONr_chiral_restr0.1280.2939
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.024399
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2640.22599
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3010.23935
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1780.2245
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2450.276
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.4030.215
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.8891.53907
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.4125994
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.32732179
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.4714.51940
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.361 139 -
Rwork0.266 2668 -
obs--94.58 %
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)
17.5680.1564-1.25593.9258-2.16563.49330.0288-0.4119-0.17090.24410.0327-0.1018-0.16220.0346-0.0614-0.18580.06050.0024-0.17370.0177-0.33859.7922.68616.563
24.44340.06951.01652.6339-1.43513.27-0.1184-0.08460.9946-0.03860.1308-0.3377-0.32640.047-0.01240.01620.0421-0.0039-0.0444-0.03110.559247.13716.96617.89
34.97620.62570.19373.1753-1.80674.2042-0.05810.54230.3861-0.09810.16480.1544-0.1279-0.1853-0.1067-0.16350.05730.0293-0.1430.0491-0.335513.87511.377-1.515
42.68120.82420.16942.2376-0.87661.82250.0640.050.0598-0.06970.0433-0.06690.10380.0353-0.1074-0.18290.076-0.0512-0.1156-0.0198-0.014948.237-2.89618.465
54.78271.24340.25174.37521.53244.26330.1497-0.0719-0.34840.52840.0118-0.44430.50980.0127-0.1615-0.1136-0.0378-0.0282-0.04910.0051-0.2891-0.2886.67966.61
65.07-0.9139-0.50255.8943-1.30812.48590.07320.3752-0.107-0.24060.04610.3343-0.1249-0.0349-0.1194-0.07590.0119-0.0323-0.1312-0.0281-0.027238.12316.49466.495
76.65430.64372.0623.6777-1.47145.93580.14580.67810.0331-0.2730.0409-0.2571-0.13110.3477-0.1867-0.1842-0.02030.02650.1115-0.0137-0.27936.65914.09649.251
84.19171.0036-0.06576.3709-0.81863.19490.19690.1626-0.87520.1930.01170.37270.2331-0.1345-0.2086-0.15280.0003-0.0797-0.2351-0.03110.208638.94-2.67173.047
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 75
2X-RAY DIFFRACTION2A84 - 190
3X-RAY DIFFRACTION3B1 - 75
4X-RAY DIFFRACTION4B84 - 190
5X-RAY DIFFRACTION5C1 - 75
6X-RAY DIFFRACTION6C84 - 188
7X-RAY DIFFRACTION7D1 - 75
8X-RAY DIFFRACTION8D84 - 190

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