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- PDB-2eb7: Crystal structure of the hypothetical regulator from Sulfolobus t... -

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Basic information

Entry
Database: PDB / ID: 2eb7
TitleCrystal structure of the hypothetical regulator from Sulfolobus tokodaii 7
Components146aa long hypothetical transcriptional regulator
KeywordsTRANSCRIPTION / transcription regulator / ST1710 / hypothetical regulator / MaR family / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homology
Function and homology information


response to stress / DNA-binding transcription factor activity / metal ion binding
Similarity search - Function
MarR family / : / MarR-type HTH domain profile. / helix_turn_helix multiple antibiotic resistance protein / MarR-type HTH domain / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
MarR family transcriptional regulator
Similarity search - Component
Biological speciesSulfolobus tokodaii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.8 Å
AuthorsKumarevel, T.S. / Nishio, M. / Shinkai, A. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: J.Struct.Biol. / Year: 2008
Title: Crystal structure of the MarR family regulatory protein, ST1710, from Sulfolobus tokodaii strain 7
Authors: Kumarevel, T. / Tanaka, T. / Nishio, M. / Gopinath, S.C.B. / Takio, K. / Shinkai, A. / Kumar, P.K.R. / Yokoyama, S.
History
DepositionFeb 7, 2007Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 6, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Derived calculations / Source and taxonomy / Version format compliance
Revision 1.2Mar 13, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 146aa long hypothetical transcriptional regulator


Theoretical massNumber of molelcules
Total (without water)16,8801
Polymers16,8801
Non-polymers00
Water2,072115
1
A: 146aa long hypothetical transcriptional regulator

A: 146aa long hypothetical transcriptional regulator


Theoretical massNumber of molelcules
Total (without water)33,7592
Polymers33,7592
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_556y,x,-z+11
Buried area6200 Å2
ΔGint-43 kcal/mol
Surface area13980 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)45.919, 45.919, 138.559
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein 146aa long hypothetical transcriptional regulator


Mass: 16879.564 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sulfolobus tokodaii (archaea) / Strain: 7 / Gene: ST1710 / Plasmid: pET21a / Production host: Escherichia coli (E. coli) / References: UniProt: Q96ZY1
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 115 / 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: 2.16 Å3/Da / Density % sol: 43.15 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 18% PEG 8000, 0.1M Sodium cacodylate, 0.2M Calcium acetate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 180 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B1 / Wavelength: 0.97896, 0.97930, 1.0000
DetectorType: RIGAKU JUPITER 210 / Detector: CCD / Date: Jul 18, 2006
RadiationMonochromator: Si / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.978961
20.97931
311
ReflectionResolution: 1.8→50 Å / Num. all: 14613 / Num. obs: 14613 / % possible obs: 99.4 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 12.7 % / Biso Wilson estimate: 26.2 Å2 / Rmerge(I) obs: 0.065
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 12.1 % / Rmerge(I) obs: 0.565 / Num. unique all: 1427 / % possible all: 99.7

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Processing

Software
NameVersionClassification
CNS1.1refinement
BSSdata collection
HKL-2000data reduction
HKL-2000data scaling
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 1.8→38.28 Å / Rfactor Rfree error: 0.01 / Data cutoff high absF: 1103215.89 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.268 718 5 %RANDOM
Rwork0.228 ---
obs0.228 14367 98.9 %-
all-14613 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 50.0859 Å2 / ksol: 0.358399 e/Å3
Displacement parametersBiso mean: 32.7 Å2
Baniso -1Baniso -2Baniso -3
1--2.41 Å20 Å20 Å2
2---2.41 Å20 Å2
3---4.82 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.28 Å0.22 Å
Luzzati d res low-5 Å
Luzzati sigma a0.09 Å0.1 Å
Refinement stepCycle: LAST / Resolution: 1.8→38.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1142 0 0 115 1257
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1
X-RAY DIFFRACTIONc_dihedral_angle_d17.6
X-RAY DIFFRACTIONc_improper_angle_d0.7
X-RAY DIFFRACTIONc_mcbond_it1.241.5
X-RAY DIFFRACTIONc_mcangle_it1.712
X-RAY DIFFRACTIONc_scbond_it2.32
X-RAY DIFFRACTIONc_scangle_it3.352.5
LS refinement shellResolution: 1.8→1.91 Å / Rfactor Rfree error: 0.024 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.279 135 5.7 %
Rwork0.255 2239 -
obs--100 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3dna-rna_rep.paramdna-rna_rep.param
X-RAY DIFFRACTION4ion.paramion.param

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