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- PDB-2efp: Crystal Structure of Tyr77 to Ala of ST1022-Glutamine Complex fro... -

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Basic information

Entry
Database: PDB / ID: 2efp
TitleCrystal Structure of Tyr77 to Ala of ST1022-Glutamine Complex from Sulolobus 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


response to amino acid / sequence-specific DNA binding / cytosol
Similarity search - Function
AsnC-type HTH domain profile. / Lrp/AsnC effector binding domain/regulation of amino acid metabolism (RAM) domain / AsnC-type HTH domain / Transcription regulator AsnC-like / helix_turn_helix ASNC type / Transcription regulator AsnC/Lrp, ligand binding domain / Lrp/AsnC ligand binding domain / Winged helix-turn-helix DNA-binding / ArsR-like helix-turn-helix domain / Dimeric alpha-beta barrel ...AsnC-type HTH domain profile. / Lrp/AsnC effector binding domain/regulation of amino acid metabolism (RAM) domain / AsnC-type HTH domain / Transcription regulator AsnC-like / helix_turn_helix ASNC type / Transcription regulator AsnC/Lrp, ligand binding domain / Lrp/AsnC 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 / Alpha-Beta Plaits / Winged helix-like DNA-binding domain superfamily / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
GLUTAMINE / Glutamine receptor protein / :
Similarity search - Component
Biological speciesSulfolobus tokodaii (archaea)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.2 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 / 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
Revision 1.4Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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)17,7234
Polymers17,4061
Non-polymers3173
Water77543
1
A: 150aa long hypothetical transcriptional regulator
hetero molecules
x 8


Theoretical massNumber of molelcules
Total (without water)141,78432
Polymers139,2518
Non-polymers2,53324
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 area33510 Å2
ΔGint-212 kcal/mol
Surface area51640 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)103.687, 103.687, 74.942
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-1043-

HOH

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Components

#1: Protein 150aa long hypothetical transcriptional regulator / ST1022


Mass: 17406.377 Da / Num. of mol.: 1 / Mutation: Y77A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sulfolobus tokodaii (archaea) / 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: Chemical ChemComp-GLN / GLUTAMINE


Type: L-peptide linking / Mass: 146.144 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H10N2O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 43 / 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: 57.47 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.2
Details: 20% PolypropyleneGlycol, 30% Isopropanol, 0.07M Sodium Citrate, 10mM Taurine, pH 6.2, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 180 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS VII / Detector: IMAGE PLATE / Date: Feb 8, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. all: 10689 / Num. obs: 10689 / % possible obs: 99.6 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 9.1 % / Biso Wilson estimate: 33.7 Å2 / Rmerge(I) obs: 0.05
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 9.2 % / Rmerge(I) obs: 0.455 / Num. unique all: 1063 / % 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

2e7w


Resolution: 2.2→19.99 Å / Rfactor Rfree error: 0.011 / Data cutoff high absF: 1934373.57 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.258 540 5.1 %RANDOM
Rwork0.232 ---
obs0.232 10634 99.7 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 45.8946 Å2 / ksol: 0.333323 e/Å3
Displacement parametersBiso mean: 51.9 Å2
Baniso -1Baniso -2Baniso -3
1--9.04 Å20 Å20 Å2
2---9.04 Å20 Å2
3---18.08 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.39 Å0.31 Å
Luzzati d res low-5 Å
Luzzati sigma a0.34 Å0.27 Å
Refinement stepCycle: LAST / Resolution: 2.2→19.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1226 0 21 43 1290
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_d23
X-RAY DIFFRACTIONc_improper_angle_d0.7
X-RAY DIFFRACTIONc_mcbond_it1.571.5
X-RAY DIFFRACTIONc_mcangle_it2.582
X-RAY DIFFRACTIONc_scbond_it2.422
X-RAY DIFFRACTIONc_scangle_it3.772.5
LS refinement shellResolution: 2.2→2.34 Å / Rfactor Rfree error: 0.037 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.365 98 5.6 %
Rwork0.284 1650 -
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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