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- PDB-2qlz: Crystal Structure of Transcription Factor PF0095 from Pyrococcus ... -

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Basic information

Entry
Database: PDB / ID: 2qlz
TitleCrystal Structure of Transcription Factor PF0095 from Pyrococcus furiosus
ComponentsTranscription Factor PF0095
KeywordsTRANSCRIPTION / Transcription factor
Function / homology
Function and homology information


DNA-binding transcription factor activity
Similarity search - Function
Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #2960 / helix_turn_helix, Arsenical Resistance Operon Repressor / HTH ArsR-type DNA-binding domain / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Helix non-globular / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Special / Arc Repressor Mutant, subunit A / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily ...Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #2960 / helix_turn_helix, Arsenical Resistance Operon Repressor / HTH ArsR-type DNA-binding domain / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Helix non-globular / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Special / 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
HTH arsR-type domain-containing protein
Similarity search - Component
Biological speciesPyrococcus furiosus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.5 Å
AuthorsYang, H. / Lipscomb, G.L. / Scott, R.A. / Rose, J.P. / Wang, B.C.
CitationJournal: To be Published
Title: Crystal Structure of Transcription Factor PF0095 from Pyrococcus furiosus
Authors: Yang, H. / Lipscomb, G.L. / Scott, R.A. / Rose, J.P. / Wang, B.C.
History
DepositionJul 13, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 29, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Transcription Factor PF0095
B: Transcription Factor PF0095
C: Transcription Factor PF0095
D: Transcription Factor PF0095


Theoretical massNumber of molelcules
Total (without water)109,1934
Polymers109,1934
Non-polymers00
Water1,802100
1
A: Transcription Factor PF0095
B: Transcription Factor PF0095


Theoretical massNumber of molelcules
Total (without water)54,5962
Polymers54,5962
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8142 Å2
MethodPISA
2
C: Transcription Factor PF0095
D: Transcription Factor PF0095


Theoretical massNumber of molelcules
Total (without water)54,5962
Polymers54,5962
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8146 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.132, 174.699, 52.249
Angle α, β, γ (deg.)90.00, 93.11, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg label comp-ID: GLU / End label comp-ID: ILE / Refine code: 5 / Auth seq-ID: 2 - 223 / Label seq-ID: 2 - 223

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB
3CC
4DD
DetailsThe biological assembly is a dimer.

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Components

#1: Protein
Transcription Factor PF0095


Mass: 27298.215 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus furiosus (archaea) / Description: SeMet labeled / Plasmid: pET24d / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus (DE3)-RIPL / References: UniProt: Q8U4J2
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 100 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.18 Å3/Da / Density % sol: 43.47 %
Crystal growTemperature: 291 K / pH: 4.4
Details: 20mM Calcium Chloride, 25% MPD, pH 4.4, modified microbatch, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 0.9724 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Feb 27, 2007 / Details: ROSENBAUM
RadiationMonochromator: SI CHANNEL 220 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9724 Å / Relative weight: 1
ReflectionResolution: 2.5→19.43 Å / Num. obs: 28832 / % possible obs: 100 % / Redundancy: 7 % / Rsym value: 0.082 / Net I/σ(I): 43.6
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 5.7 % / Mean I/σ(I) obs: 5 / Rsym value: 0.32 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
SERGUIdata collection
HKL-2000data reduction
HKL-2000data scaling
SOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 2.5→19.43 Å / Cor.coef. Fo:Fc: 0.91 / Cor.coef. Fo:Fc free: 0.868 / SU B: 10.471 / SU ML: 0.239 / Cross valid method: THROUGHOUT / ESU R: 1.982 / ESU R Free: 0.341
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27132 1484 4.9 %RANDOM
Rwork0.22571 ---
obs0.22791 28832 100 %-
all-2038 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 28.146 Å2
Baniso -1Baniso -2Baniso -3
1-0.02 Å20 Å2-0.06 Å2
2--0 Å20 Å2
3----0.03 Å2
Refinement stepCycle: LAST / Resolution: 2.5→19.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6959 0 0 100 7059
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0227061
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.251.9939503
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5635857
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.01424.503302
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.858151391
X-RAY DIFFRACTIONr_dihedral_angle_4_deg25.6531539
X-RAY DIFFRACTIONr_chiral_restr0.0910.21118
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.025043
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2040.23126
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.2980.24832
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1570.2217
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2470.283
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2080.211
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.6531.54458
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.03926987
X-RAY DIFFRACTIONr_scbond_it1.14132935
X-RAY DIFFRACTIONr_scangle_it1.7654.52516
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A828medium positional0.390.5
2B828medium positional0.460.5
3C828medium positional0.490.5
4D828medium positional0.330.5
1A812loose positional0.785
2B812loose positional0.855
3C812loose positional0.945
4D812loose positional0.795
1A828medium thermal0.792
2B828medium thermal0.542
3C828medium thermal0.62
4D828medium thermal0.482
1A812loose thermal1.4610
2B812loose thermal1.0310
3C812loose thermal1.3210
4D812loose thermal1.0410
LS refinement shellResolution: 2.5→2.564 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.285 111 -
Rwork0.237 2038 -
obs--100 %

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