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- PDB-1i1g: CRYSTAL STRUCTURE OF THE LRP-LIKE TRANSCRIPTIONAL REGULATOR FROM ... -

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Basic information

Entry
Database: PDB / ID: 1i1g
TitleCRYSTAL STRUCTURE OF THE LRP-LIKE TRANSCRIPTIONAL REGULATOR FROM THE ARCHAEON PYROCOCCUS FURIOSUS
ComponentsTRANSCRIPTIONAL REGULATOR LRPA
KeywordsTRANSCRIPTION / helix-turn-helix / Lrp/AsnC family / Pyrococcus furiosus / transcriptional regulator
Function / homology
Function and homology information


sequence-specific DNA binding
Similarity search - Function
: / Transcription regulator HTH, AsnC-type, conserved site / AsnC-type HTH domain signature. / : / 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 ...: / Transcription regulator HTH, AsnC-type, conserved site / AsnC-type HTH domain signature. / : / 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
HTH-type transcriptional regulator LrpA
Similarity search - Component
Biological speciesPyrococcus furiosus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 2.9 Å
AuthorsLeonard, P.M. / Smits, S.H.J. / Sedelnikova, S.E. / Brinkman, A.B. / de Vos, W.M. / van der Oost, J. / Rice, D.W. / Rafferty, J.B.
CitationJournal: EMBO J. / Year: 2001
Title: Crystal structure of the Lrp-like transcriptional regulator from the archaeon Pyrococcus furiosus.
Authors: Leonard, P.M. / Smits, S.H. / Sedelnikova, S.E. / Brinkman, A.B. / de Vos, W.M. / van der Oost, J. / Rice, D.W. / Rafferty, J.B.
History
DepositionFeb 1, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 6, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Remark 300 BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 2 ... BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 2 CHAIN(S). SEE REMARK 350 FOR INFORMATION ON GENERATING THE BIOLOGICAL MOLECULE(S). AT PRESENT IT IS UNCLEAR WHETHER THE BIOLOGICAL UNIT IS A DIMER OR OCTAMER. COORDINATES FOR A COMPLETE BIOLOGICAL DIMER CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS ONE AND FOUR LISTED IN REMARK 350 TO SUBUNIT A IN THE ASYMMETRIC UNIT, OR BY APPLYING BIOMT TRANSFORMATIONS ONE AND THREE TO SUBUNIT B. COORDINATES FOR A COMPLETE BIOLOGICAL OCTAMER CAN BE GENERATED BY APPLYING ALL FOUR BIOMT TRANSFORMATIONS TO SUBUNITS A AND B IN THE ASYMMETRIC UNIT.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: TRANSCRIPTIONAL REGULATOR LRPA
B: TRANSCRIPTIONAL REGULATOR LRPA


Theoretical massNumber of molelcules
Total (without water)31,8362
Polymers31,8362
Non-polymers00
Water00
1
A: TRANSCRIPTIONAL REGULATOR LRPA
B: TRANSCRIPTIONAL REGULATOR LRPA

A: TRANSCRIPTIONAL REGULATOR LRPA
B: TRANSCRIPTIONAL REGULATOR LRPA

A: TRANSCRIPTIONAL REGULATOR LRPA
B: TRANSCRIPTIONAL REGULATOR LRPA

A: TRANSCRIPTIONAL REGULATOR LRPA
B: TRANSCRIPTIONAL REGULATOR LRPA


Theoretical massNumber of molelcules
Total (without water)127,3428
Polymers127,3428
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555-y,-x,-z1
crystal symmetry operation10_555-x,-y,z1
crystal symmetry operation15_555y,x,-z1
Buried area27330 Å2
ΔGint-186 kcal/mol
Surface area47810 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)101.318, 101.318, 245.361
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number98
Space group name H-MI4122

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Components

#1: Protein TRANSCRIPTIONAL REGULATOR LRPA


Mass: 15917.790 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus furiosus (archaea) / Production host: Escherichia coli (E. coli) / References: UniProt: P42180

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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: 4.94 Å3/Da / Density % sol: 75.12 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 6
Details: ammonium sulphate, sodium citrate, pH 6, VAPOR DIFFUSION, HANGING DROP, temperature 290K
Crystal grow
*PLUS
pH: 5.3 / Method: vapor diffusion
Details: Sedelnikova, S.E., (2001) Acta Crystallogr, D57, 886.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
110 mg/mlprotein1drop
220 mMsodium acetate1droppH5.3
30.25 M1dropNaCl
42.4-3.6 Mammonium sulfate1reservoir
50.1 Msodium citrate1reservoirpH6.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX7.2 / Wavelength: 1.488 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Sep 4, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.488 Å / Relative weight: 1
ReflectionResolution: 2.9→20 Å / Num. all: 13809 / Num. obs: 13809 / % possible obs: 94.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.2 % / Biso Wilson estimate: 73.6 Å2 / Rmerge(I) obs: 0.065 / Net I/σ(I): 14.7
Reflection shellResolution: 2.9→2.97 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.346 / % possible all: 94.7
Reflection
*PLUS
Lowest resolution: 20 Å / Num. measured all: 30436
Reflection shell
*PLUS
% possible obs: 96.2 %

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Processing

Software
NameClassification
MLPHAREphasing
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MIR / Resolution: 2.9→20 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.382 134 Random
Rwork0.313 --
all0.316 13354 -
obs0.316 12686 -
Refinement stepCycle: LAST / Resolution: 2.9→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2138 0 0 0 2138
Software
*PLUS
Name: REFMAC / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.9 Å / Lowest resolution: 20 Å / σ(F): 0
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.012
X-RAY DIFFRACTIONp_angle_d
X-RAY DIFFRACTIONp_angle_deg3
X-RAY DIFFRACTIONp_dihedral_angle_d
X-RAY DIFFRACTIONp_improper_angle_d
X-RAY DIFFRACTIONp_mcbond_it
X-RAY DIFFRACTIONp_scbond_it
X-RAY DIFFRACTIONp_mcangle_it
X-RAY DIFFRACTIONp_scangle_it

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