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- PDB-2e1c: Structure of Putative HTH-type transcriptional regulator PH1519/D... -

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Basic information

Entry
Database: PDB / ID: 2e1c
TitleStructure of Putative HTH-type transcriptional regulator PH1519/DNA Complex
Components
  • DNA (5'-D(*DAP*DGP*DTP*DGP*DAP*DAP*DAP*DAP*DTP*DTP*DTP*DTP*DTP*DCP*DAP*DCP*DA)-3')
  • DNA (5'-D(*DTP*DGP*DTP*DGP*DAP*DAP*DAP*DAP*DAP*DTP*DTP*DTP*DTP*DCP*DAP*DCP*DT)-3')
  • Putative HTH-type transcriptional regulator PH1519
KeywordsTRANSCRIPTION/DNA / DNA-binding / transcriptional regulatory protein / archaeal / TRANSCRIPTION-DNA COMPLEX
Function / homology
Function and homology information


sequence-specific DNA binding / identical protein binding
Similarity search - Function
AsnC-type helix-turn-helix domain / AsnC-type HTH domain profile. / Lrp/AsnC effector binding domain/regulation of amino acid metabolism (RAM) domain / Transcription regulator AsnC-like / helix_turn_helix ASNC type / AsnC-type HTH domain / Transcription regulator AsnC/Lrp, ligand binding domain / Lrp/AsnC ligand binding domain / ArsR-like helix-turn-helix domain / Dimeric alpha-beta barrel ...AsnC-type helix-turn-helix domain / AsnC-type HTH domain profile. / Lrp/AsnC effector binding domain/regulation of amino acid metabolism (RAM) domain / Transcription regulator AsnC-like / helix_turn_helix ASNC type / AsnC-type HTH domain / Transcription regulator AsnC/Lrp, ligand binding domain / Lrp/AsnC ligand binding domain / 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
DNA / DNA (> 10) / HTH-type transcriptional regulator FL11
Similarity search - Component
Biological speciesPyrococcus horikoshii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsKoike, H. / Suzuki, M.
CitationJournal: Structure / Year: 2007
Title: Feast/Famine Regulation by Transcription Factor FL11 for the Survival of the Hyperthermophilic Archaeon Pyrococcus OT3.
Authors: Yokoyama, K. / Ishijima, S.A. / Koike, H. / Kurihara, C. / Shimowasa, A. / Kabasawa, M. / Kawashima, T. / Suzuki, M.
History
DepositionOct 24, 2006Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 4, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.2Jul 19, 2017Group: Derived calculations
Category: pdbx_struct_assembly / pdbx_struct_assembly_gen ...pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_oper_list / struct_conn
Item: _pdbx_struct_assembly.oligomeric_count / _pdbx_struct_assembly.oligomeric_details ..._pdbx_struct_assembly.oligomeric_count / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_assembly_gen.oper_expression / _pdbx_struct_oper_list.matrix[1][1] / _pdbx_struct_oper_list.matrix[3][3] / _pdbx_struct_oper_list.name / _pdbx_struct_oper_list.symmetry_operation / _pdbx_struct_oper_list.type / _pdbx_struct_oper_list.vector[1]
Revision 1.3Oct 25, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: DNA (5'-D(*DAP*DGP*DTP*DGP*DAP*DAP*DAP*DAP*DTP*DTP*DTP*DTP*DTP*DCP*DAP*DCP*DA)-3')
D: DNA (5'-D(*DTP*DGP*DTP*DGP*DAP*DAP*DAP*DAP*DAP*DTP*DTP*DTP*DTP*DCP*DAP*DCP*DT)-3')
A: Putative HTH-type transcriptional regulator PH1519


Theoretical massNumber of molelcules
Total (without water)29,5613
Polymers29,5613
Non-polymers00
Water2,396133
1
B: DNA (5'-D(*DAP*DGP*DTP*DGP*DAP*DAP*DAP*DAP*DTP*DTP*DTP*DTP*DTP*DCP*DAP*DCP*DA)-3')
D: DNA (5'-D(*DTP*DGP*DTP*DGP*DAP*DAP*DAP*DAP*DAP*DTP*DTP*DTP*DTP*DCP*DAP*DCP*DT)-3')

A: Putative HTH-type transcriptional regulator PH1519

A: Putative HTH-type transcriptional regulator PH1519


Theoretical massNumber of molelcules
Total (without water)48,7124
Polymers48,7124
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z2
crystal symmetry operation7_555-x+1/2,y,-z1
Unit cell
Length a, b, c (Å)68.41, 92.35, 109.19
Angle α, β, γ (deg.)90, 90, 90
Int Tables number24
Space group name H-MI212121
Number of models2

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Components

#1: DNA chain DNA (5'-D(*DAP*DGP*DTP*DGP*DAP*DAP*DAP*DAP*DTP*DTP*DTP*DTP*DTP*DCP*DAP*DCP*DA)-3')


Mass: 5209.422 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: DNA chain DNA (5'-D(*DTP*DGP*DTP*DGP*DAP*DAP*DAP*DAP*DAP*DTP*DTP*DTP*DTP*DCP*DAP*DCP*DT)-3')


Mass: 5200.408 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: Protein Putative HTH-type transcriptional regulator PH1519 / Lrp/AsnC family protein


Mass: 19151.221 Da / Num. of mol.: 1 / Fragment: residues 24-170
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus horikoshii (archaea) / Strain: OT3 / Plasmid: pET28a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: O59188
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 133 / 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: 2.88 Å3/Da / Density % sol: 57.34 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 875mM ammonium sulfate, 10mM magnesium chloride, 20mM sodium chloride, 100mM MES buffer, 5% glycerol, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Components of the solutions
IDNameCrystal-IDSol-ID
1ammonium sulfate11
2magnesium chloride11
3sodium chloride11
4MES11
5glycerol11
6H2O11
7ammonium sulfate12
8magnesium chloride12
9sodium chloride12
10MES12
11glycerol12
12H2O12

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 3, 2006
RadiationMonochromator: Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.1→55 Å / Num. obs: 20389 / % possible obs: 99.2 % / Observed criterion σ(I): 3 / Redundancy: 6 % / Rmerge(I) obs: 0.079 / Net I/σ(I): 5.6
Reflection shellResolution: 2.1→2.21 Å / Redundancy: 6.2 % / Rmerge(I) obs: 0.456 / Mean I/σ(I) obs: 1.6 / Num. unique all: 2956 / % possible all: 100

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
AMoREphasing
CNS1.1refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1RI7

1ri7


Resolution: 2.1→55 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.23 1049 -RANDOM
Rwork0.206 ---
obs-19340 99.2 %-
Refine analyze
FreeObs
Luzzati coordinate error0.3 Å0.26 Å
Luzzati d res low-5 Å
Luzzati sigma a0.37 Å0.34 Å
Refinement stepCycle: LAST / Resolution: 2.1→55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1155 691 0 133 1979
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.12739
X-RAY DIFFRACTIONc_bond_d0.004776

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