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- PDB-2zcx: Crystal structure of TetR family transcriptional regulator SCO7815 -

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Basic information

Entry
Database: PDB / ID: 2zcx
TitleCrystal structure of TetR family transcriptional regulator SCO7815
ComponentsTetR-family transcriptional regulator
KeywordsTRANSCRIPTION / TetR family / helix-turn-helix / DNA-binding / transcription regulation
Function / homology
Function and homology information


transcription cis-regulatory region binding / DNA-binding transcription factor activity / regulation of DNA-templated transcription
Similarity search - Function
Tetracyclin repressor-like, C-terminal domain 34 / Tetracyclin repressor-like, C-terminal domain / : / Tetracycline Repressor, domain 2 / 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
TetR-family transcriptional regulator
Similarity search - Component
Biological speciesStreptomyces coelicolor (bacteria)
MethodX-RAY DIFFRACTION / SAD / Resolution: 2.22 Å
AuthorsOkada, U. / Kondo, K. / Yao, M. / Watanabe, N. / Tanaka, I.
CitationJournal: To be Published
Title: Structural and functional analysis of TetR family transcriptional regulator SCO7815
Authors: Okada, U. / Kondo, K. / Hayashi, T. / Watanabe, N. / Yao, M. / Tamura, T. / Tanaka, I.
History
DepositionNov 13, 2007Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 18, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 13, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Remark 650HELIX DETERMINATION METHOD: AUTHOR DETERMINED

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: TetR-family transcriptional regulator


Theoretical massNumber of molelcules
Total (without water)25,4451
Polymers25,4451
Non-polymers00
Water2,162120
1
A: TetR-family transcriptional regulator

A: TetR-family transcriptional regulator


Theoretical massNumber of molelcules
Total (without water)50,8902
Polymers50,8902
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area4530 Å2
ΔGint-25.9 kcal/mol
Surface area17370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.068, 72.068, 90.424
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11A-346-

HOH

21A-348-

HOH

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Components

#1: Protein TetR-family transcriptional regulator / SCO7815


Mass: 25445.021 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces coelicolor (bacteria) / Strain: A3(2) / Gene: SCO7815 / Plasmid: pTip / Production host: Rhodococcus erythropolis (bacteria) / Strain (production host): L88 / References: UniProt: Q9FBX0
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 120 / 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: 2.31 Å3/Da / Density % sol: 46.69 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.8M potassium sodium tartrate, 0.1M Tris-HCl, 1% PEG5000MME, pH8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 2.29 Å
DetectorType: RIGAKU RAXIS VII / Detector: IMAGE PLATE / Date: Oct 13, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 2.29 Å / Relative weight: 1
ReflectionResolution: 2.22→50 Å / Num. obs: 12269 / % possible obs: 99.6 % / Redundancy: 27 % / Biso Wilson estimate: 54.463 Å2 / Rmerge(I) obs: 0.06 / Rsym value: 0.06 / Net I/σ(I): 45.705
Reflection shellResolution: 2.22→2.3 Å / Redundancy: 22.6 % / Rmerge(I) obs: 0.43 / Mean I/σ(I) obs: 8.064 / Num. unique all: 1158 / Rsym value: 0.43 / % possible all: 100

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Processing

Software
NameVersionClassification
CrystalCleardata collection
SHELXSphasing
CNS1.1refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 2.22→20 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2475 616 -random
Rwork0.222 ---
obs-12248 99.7 %-
Displacement parametersBiso mean: 52.3 Å2
Baniso -1Baniso -2Baniso -3
1--0.866 Å20 Å20 Å2
2---0.866 Å20 Å2
3---1.731 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.38 Å0.3 Å
Luzzati d res low-5 Å
Luzzati sigma a0.3 Å0.21 Å
Refinement stepCycle: LAST / Resolution: 2.22→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1574 0 0 120 1694
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.0059
X-RAY DIFFRACTIONc_angle_deg1.17
X-RAY DIFFRACTIONc_dihedral_angle_d18.29
X-RAY DIFFRACTIONc_improper_angle_d0.738
LS refinement shellResolution: 2.22→2.3 Å
RfactorNum. reflection% reflection
Rfree0.32 56 -
Rwork0.383 --
obs-1158 96.91 %

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