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- PDB-2cyy: Crystal structure of PH1519 from Pyrococcus horikosii OT3 -

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Basic information

Entry
Database: PDB / ID: 2cyy
TitleCrystal structure of PH1519 from Pyrococcus horikosii OT3
ComponentsPutative HTH-type transcriptional regulator PH1519
KeywordsDNA BINDING PROTEIN / structural genomics / Pyrococcus horikosii OT3 / 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 / identical protein binding
Similarity search - Function
AsnC-type helix-turn-helix domain / 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 / Lrp/AsnC ligand binding domain / Transcription regulator AsnC/Lrp, ligand binding domain / AsnC-type HTH domain / ArsR-like helix-turn-helix domain / Dimeric alpha-beta barrel ...AsnC-type helix-turn-helix domain / 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 / Lrp/AsnC ligand binding domain / Transcription regulator AsnC/Lrp, ligand binding domain / AsnC-type HTH domain / ArsR-like helix-turn-helix domain / Dimeric alpha-beta barrel / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Winged helix DNA-binding domain superfamily / Arc Repressor Mutant, subunit A / Winged helix-like DNA-binding domain superfamily / Alpha-Beta Plaits / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
GLUTAMINE / HTH-type transcriptional regulator FL11
Similarity search - Component
Biological speciesPyrococcus horikoshii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.8 Å
AuthorsOkazaki, N. / Nakano, N. / Shinkai, A. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: To be Published
Title: Crystal structure of PH1519 from Pyrococcus horikosii OT3
Authors: Okazaki, N. / Nakano, N. / Shinkai, A. / Yokoyama, S.
History
DepositionJul 8, 2005Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 19, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Putative HTH-type transcriptional regulator PH1519
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,4746
Polymers17,1671
Non-polymers3065
Water3,855214
1
A: Putative HTH-type transcriptional regulator PH1519
hetero molecules

A: Putative HTH-type transcriptional regulator PH1519
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,94812
Polymers34,3352
Non-polymers61310
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation11_555-x+y,y,-z+1/21
Buried area7090 Å2
ΔGint-90 kcal/mol
Surface area14890 Å2
MethodPISA
2


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)130.573, 130.573, 47.716
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122
Components on special symmetry positions
IDModelComponents
11A-2003-

CA

21A-2094-

HOH

31A-2148-

HOH

41A-2153-

HOH

51A-2154-

HOH

61A-2164-

HOH

71A-2165-

HOH

81A-2166-

HOH

91A-2167-

HOH

101A-2197-

HOH

111A-2206-

HOH

DetailsThe second part of the biological assembly is generated by the two fold axis: -x+y, y,-z+1/2.

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Components

#1: Protein Putative HTH-type transcriptional regulator PH1519


Mass: 17167.434 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus horikoshii (archaea) / Plasmid: pET11a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus(DE3)-RIL-X / References: UniProt: O59188
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-GLN / GLUTAMINE / Glutamine


Type: L-peptide linking / Mass: 146.144 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H10N2O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 214 / 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: 3.42 Å3/Da / Density % sol: 64.02 %
Crystal growTemperature: 291 K / Method: microbatch / pH: 8.5
Details: 25.5% PEG4000, 0.085M Tris-HCl, 0.17M Li2(SO4), 15% Glycerol, pH 8.5, Microbatch, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B2 / Wavelength: 0.97901, 0.97940, 0.96000
DetectorType: RIGAKU JUPITER 210 / Detector: CCD / Date: Oct 26, 2004 / Details: mirrors
RadiationMonochromator: Bending Magnet / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.979011
20.97941
30.961
ReflectionResolution: 1.8→30 Å / Num. all: 22776 / Num. obs: 22776 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 23.1 % / Biso Wilson estimate: 18.612 Å2 / Rmerge(I) obs: 0.076 / Rsym value: 0.062 / Net I/σ(I): 17.1
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 21.9 % / Rmerge(I) obs: 0.354 / Mean I/σ(I) obs: 8.84 / Num. unique all: 2239 / Rsym value: 0.341 / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-2000data collection
SCALEPACKdata scaling
SOLVEphasing
CNS1.1refinement
HKL-2000data reduction
RefinementMethod to determine structure: MAD / Resolution: 1.8→29.58 Å / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHPUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.245 1138 -RANDOM
Rwork0.219 ---
all0.22 22717 --
obs0.22 22717 99.8 %-
Displacement parametersBiso mean: 26.2 Å2
Baniso -1Baniso -2Baniso -3
1--2.72 Å2-0.9 Å20 Å2
2---2.72 Å20 Å2
3---5.45 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.25 Å0.21 Å
Luzzati d res low-5 Å
Luzzati sigma a0.1 Å0.09 Å
Refinement stepCycle: LAST / Resolution: 1.8→29.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1191 0 14 214 1419
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d22.4
X-RAY DIFFRACTIONc_improper_angle_d0.76
LS refinement shellResolution: 1.8→1.88 Å / Rfactor Rfree error: 0.02
RfactorNum. reflection% reflection
Rfree0.247 151 -
Rwork0.239 --
obs-2780 100 %

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