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- PDB-3eup: The crystal structure of the transcriptional regulator, TetR fami... -

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Basic information

Entry
Database: PDB / ID: 3eup
TitleThe crystal structure of the transcriptional regulator, TetR family from Cytophaga hutchinsonii
ComponentsTranscriptional regulator, TetR family
KeywordsTranscription regulator / Transcriptional regulator / TetR family / Structural genomics / PSI2 / MCSG / Protein Structure Initiative / Midwest Center for Structural Genomics / Transcription / Transcription regulation
Function / homology
Function and homology information


Tetracycline Repressor, domain 2 / Tetracyclin repressor-like, C-terminal domain superfamily / Tetracycline Repressor; domain 2 / Bacterial regulatory proteins, tetR family / DNA-binding HTH domain, TetR-type / TetR-type HTH domain profile. / Homeobox-like domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Transcriptional regulator, TetR family
Similarity search - Component
Biological speciesCytophaga hutchinsonii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.99 Å
AuthorsZhang, R. / Bigelow, L. / Abdullah, J. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: The crystal structure of the transcriptional regulator, TetR family from Cytophaga hutchinsonii
Authors: Zhang, R. / Bigelow, L. / Abdullah, J. / Joachimiak, A.
History
DepositionOct 10, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 25, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Refinement description ...Advisory / Refinement description / Source and taxonomy / Version format compliance
Revision 1.2Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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

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Assembly

Deposited unit
A: Transcriptional regulator, TetR family
B: Transcriptional regulator, TetR family
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,2024
Polymers45,0102
Non-polymers1922
Water4,702261
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4160 Å2
ΔGint-69 kcal/mol
Surface area18300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.595, 53.400, 178.005
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsThis protein existed as dimer. The deposited MolA/MolB represent the dimer in the asymmetric unit.

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Components

#1: Protein Transcriptional regulator, TetR family


Mass: 22504.789 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Cytophaga hutchinsonii (bacteria) / Strain: ATCC 33406 / Gene: CHU_2862, envR, gi:110639243 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q11R54
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 261 / 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: 2.41 Å3/Da / Density % sol: 48.9 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 25% PEG4000, 0.1M MES, 0.2M MgCl2, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9794 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 3, 2007 / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 1.99→89.09 Å / Num. all: 29006 / Num. obs: 28745 / % possible obs: 99.1 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 9.2 % / Biso Wilson estimate: 22 Å2 / Rmerge(I) obs: 0.11 / Net I/σ(I): 31.62
Reflection shellResolution: 2→2.046 Å / Redundancy: 8.3 % / Rmerge(I) obs: 0.67 / Mean I/σ(I) obs: 2.76 / Num. unique all: 2208 / % possible all: 94.47

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Processing

Software
NameVersionClassification
SBC-Collectdata collection
HKL-3000phasing
REFMAC5.5.0054refinement
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: SAD / Resolution: 1.99→89.09 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.934 / SU B: 8.067 / SU ML: 0.104 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.176 / ESU R Free: 0.161
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22937 1531 5.1 %RANDOM
Rwork0.18227 ---
obs0.18463 28745 99.1 %-
all-29006 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 21.411 Å2
Baniso -1Baniso -2Baniso -3
1-1.88 Å20 Å20 Å2
2---0.42 Å20 Å2
3----1.46 Å2
Refinement stepCycle: LAST / Resolution: 1.99→89.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3116 0 10 261 3387
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0223174
X-RAY DIFFRACTIONr_bond_other_d0.0010.022116
X-RAY DIFFRACTIONr_angle_refined_deg1.6311.9654290
X-RAY DIFFRACTIONr_angle_other_deg0.96335205
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2085401
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.8825128
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.48415577
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.7731512
X-RAY DIFFRACTIONr_chiral_restr0.0860.2503
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.023479
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02609
X-RAY DIFFRACTIONr_mcbond_it0.8151.51997
X-RAY DIFFRACTIONr_mcbond_other0.2341.5820
X-RAY DIFFRACTIONr_mcangle_it1.54523214
X-RAY DIFFRACTIONr_scbond_it3.17831177
X-RAY DIFFRACTIONr_scangle_it4.6844.51076
LS refinement shellResolution: 1.994→2.046 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.27 99 -
Rwork0.229 1987 -
obs-2086 94.47 %
Refinement TLS params.Method: refined / Origin x: 0.277 Å / Origin y: 25.947 Å / Origin z: 20.337 Å
111213212223313233
T0.0768 Å2-0.0291 Å2-0.0194 Å2-0.0903 Å20.0133 Å2--0.0106 Å2
L1.0848 °2-0.1674 °20.1187 °2-0.564 °2-0.1017 °2--1.0524 °2
S-0.0536 Å °0.0995 Å °0.083 Å °-0.1154 Å °0.037 Å °0.0297 Å °0.0264 Å °0.0071 Å °0.0166 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-1 - 50
2X-RAY DIFFRACTION1A51 - 100
3X-RAY DIFFRACTION1A101 - 150
4X-RAY DIFFRACTION1A151 - 201
5X-RAY DIFFRACTION1B2 - 50
6X-RAY DIFFRACTION1B51 - 100
7X-RAY DIFFRACTION1B101 - 150
8X-RAY DIFFRACTION1B151 - 201

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