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- PDB-3v68: Crystal structure of Pyrococcus furiosus PF2050, a member of DUF2... -

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Basic information

Entry
Database: PDB / ID: 3v68
TitleCrystal structure of Pyrococcus furiosus PF2050, a member of DUF2666 family protein
ComponentsPutative uncharacterized protein
KeywordsDNA BINDING PROTEIN / DUF2666 / double stranded DNA
Function / homologyDomain of unknown function DUF2666 / Domain of unknown function (DUF2666) / DUF2666 domain-containing protein
Function and homology information
Biological speciesPyrococcus furiosus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.56 Å
AuthorsHan, B.G. / Lee, B.I.
CitationJournal: Febs Lett. / Year: 2012
Title: Crystal structure of Pyrococcus furiosus PF2050, a member of the DUF2666 protein family
Authors: Han, B.G. / Jeong, K.C. / Cho, J.W. / Jeong, B.C. / Song, H.K. / Lee, J.Y. / Shin, D.H. / Lee, S. / Lee, B.I.
History
DepositionDec 19, 2011Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 18, 2012Provider: repository / Type: Initial release
Revision 1.1Jun 26, 2013Group: Database references
Revision 1.2Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Putative uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,0642
Polymers28,9461
Non-polymers1181
Water4,414245
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)41.722, 66.531, 46.372
Angle α, β, γ (deg.)90.00, 96.56, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Putative uncharacterized protein / PF2050 protein


Mass: 28945.748 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus furiosus (archaea) / Strain: DSM 3638 / Gene: PF2050 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8TZE5
#2: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 245 / 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: 2.21 Å3/Da / Density % sol: 44.32 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 0.02M calcium chloride dehydrate, 0.1M sodium acetate trihydrate, 30% 2-methyl-2,4-pentanediol, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1.0000, 0.97910, 0.97924, 0.9600
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Mar 10, 2011
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
111
20.97911
30.979241
40.961
ReflectionResolution: 1.56→50 Å / Num. all: 34223 / Num. obs: 32515 / % possible obs: 94.8 %

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Processing

Software
NameVersionClassification
HKL-2000data collection
SOLVEphasing
REFMAC5.5.0110refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MAD / Resolution: 1.56→46.07 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.929 / SU B: 1.458 / SU ML: 0.054 / Cross valid method: THROUGHOUT / ESU R: 0.1 / ESU R Free: 0.096 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22493 1686 4.9 %RANDOM
Rwork0.19771 ---
obs0.19909 32515 94.73 %-
all-34223 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 19.32 Å2
Baniso -1Baniso -2Baniso -3
1--0.17 Å20 Å20.05 Å2
2--0.96 Å20 Å2
3----0.78 Å2
Refinement stepCycle: LAST / Resolution: 1.56→46.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2009 0 8 245 2262
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0222073
X-RAY DIFFRACTIONr_angle_refined_deg0.9591.9972783
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.6365253
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.64225.05591
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.11715435
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.9361512
X-RAY DIFFRACTIONr_chiral_restr0.0680.2316
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0211489
X-RAY DIFFRACTIONr_mcbond_it0.5071.51250
X-RAY DIFFRACTIONr_mcangle_it0.99922032
X-RAY DIFFRACTIONr_scbond_it1.5013823
X-RAY DIFFRACTIONr_scangle_it2.6414.5751
LS refinement shellResolution: 1.557→1.597 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.284 99 -
Rwork0.233 1945 -
obs--76.84 %

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