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- PDB-2efo: Crystal structure of Tyr77 to Ala of ST1022 from Sulfolobus tokodaii 7 -

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Basic information

Entry
Database: PDB / ID: 2efo
TitleCrystal structure of Tyr77 to Ala of ST1022 from Sulfolobus tokodaii 7
Components150aa long hypothetical transcriptional regulator
KeywordsTRANSCRIPTION REGULATOR / Transcriptional regulator / Lrp/AsnC family Gln binding / ST1022 / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homology
Function and homology information


sequence-specific DNA binding
Similarity search - Function
AsnC-type HTH domain profile. / Transcription regulator AsnC-like / helix_turn_helix ASNC type / Lrp/AsnC effector binding domain/regulation of amino acid metabolism (RAM) domain / AsnC-type HTH domain / Lrp/AsnC ligand binding domain / Transcription regulator AsnC/Lrp, ligand binding domain / Winged helix-turn-helix DNA-binding / ArsR-like helix-turn-helix domain / Dimeric alpha-beta barrel ...AsnC-type HTH domain profile. / Transcription regulator AsnC-like / helix_turn_helix ASNC type / Lrp/AsnC effector binding domain/regulation of amino acid metabolism (RAM) domain / AsnC-type HTH domain / Lrp/AsnC ligand binding domain / Transcription regulator AsnC/Lrp, ligand binding domain / Winged helix-turn-helix DNA-binding / ArsR-like helix-turn-helix domain / Dimeric alpha-beta barrel / 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 / Alpha-Beta Plaits / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Glutamine receptor protein / :
Similarity search - Component
Biological speciesSulfolobus tokodaii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsKumarevel, T.S. / Karthe, P. / Nakano, N. / Shinkai, A. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: Nucleic Acids Res. / Year: 2008
Title: Crystal structure of glutamine receptor protein from Sulfolobus tokodaii strain 7 in complex with its effector L-glutamine: implications of effector binding in molecular association and DNA binding.
Authors: Kumarevel, T.S. / Nakano, N. / Ponnuraj, K. / Gopinath, S.C. / Sakamoto, K. / Shinkai, A. / Kumar, P.K. / Yokoyama, S.
History
DepositionFeb 23, 2007Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 26, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Derived calculations / Source and taxonomy / Version format compliance
Revision 1.2Oct 11, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Nov 10, 2021Group: Database references / Derived calculations / Category: 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: 150aa long hypothetical transcriptional regulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,4312
Polymers17,4061
Non-polymers241
Water1,04558
1
A: 150aa long hypothetical transcriptional regulator
hetero molecules
x 8


Theoretical massNumber of molelcules
Total (without water)139,44516
Polymers139,2518
Non-polymers1948
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_555-y,x,z1
crystal symmetry operation4_555y,-x,z1
crystal symmetry operation5_555-x,y,-z1
crystal symmetry operation6_555x,-y,-z1
crystal symmetry operation7_555y,x,-z1
crystal symmetry operation8_555-y,-x,-z1
Buried area32130 Å2
ΔGint-216 kcal/mol
Surface area49700 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)103.902, 103.902, 74.483
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number97
Space group name H-MI422
Components on special symmetry positions
IDModelComponents
11A-1001-

MG

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Components

#1: Protein 150aa long hypothetical transcriptional regulator


Mass: 17406.377 Da / Num. of mol.: 1 / Mutation: Y77A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sulfolobus tokodaii (archaea) / Strain: 7 / Gene: ST1022 / Plasmid: pET21a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q972W6, UniProt: F9VNT4*PLUS
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 58 / 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: 2.89 Å3/Da / Density % sol: 57.39 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.2
Details: 20% PolypropyleneGlycol, 30% Isopropanol, 0.07M Sodium citrate, 200mM ndSb-221, pH 6.2, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 180 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL45XU / Wavelength: 0.9794 Å
DetectorType: RIGAKU JUPITER 210 / Detector: CCD / Date: Oct 7, 2006
RadiationMonochromator: Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. all: 10745 / Num. obs: 10745 / % possible obs: 99.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 14.6 % / Biso Wilson estimate: 31.2 Å2 / Rmerge(I) obs: 0.092
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 14.9 % / Rmerge(I) obs: 0.488 / Num. unique all: 1042 / % possible all: 100

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Processing

Software
NameVersionClassification
CNS1.1refinement
BSSdata collection
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2E7W
Resolution: 2.4→19.71 Å / Rfactor Rfree error: 0.011 / Data cutoff high absF: 2423793.95 / 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
Rfree0.264 600 7.3 %RANDOM
Rwork0.229 ---
obs0.229 8231 99.9 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 42.6 Å2 / ksol: 0.317088 e/Å3
Displacement parametersBiso mean: 54.6 Å2
Baniso -1Baniso -2Baniso -3
1--17.7 Å20 Å20 Å2
2---17.7 Å20 Å2
3---35.41 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.43 Å0.35 Å
Luzzati d res low-5 Å
Luzzati sigma a0.53 Å0.49 Å
Refinement stepCycle: LAST / Resolution: 2.4→19.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1214 0 1 58 1273
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d22.2
X-RAY DIFFRACTIONc_improper_angle_d0.72
X-RAY DIFFRACTIONc_mcbond_it1.421.5
X-RAY DIFFRACTIONc_mcangle_it2.462
X-RAY DIFFRACTIONc_scbond_it2.112
X-RAY DIFFRACTIONc_scangle_it3.392.5
LS refinement shellResolution: 2.4→2.55 Å / Rfactor Rfree error: 0.039 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.364 87 6.5 %
Rwork0.371 1253 -
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.top
X-RAY DIFFRACTION4ion.paramion.top

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