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- PDB-4o8u: Structure of PF2046 -

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Basic information

Entry
Database: PDB / ID: 4o8u
TitleStructure of PF2046
ComponentsUncharacterized protein PF2046
KeywordsUNKNOWN FUNCTION / low resolution diffraction / PF2046 / B-factorsharpening / homodimer of trimers
Function / homologyProtein of unknown function DUF4152 / Protein of unknown function DUF4152 / Protein of unknown function (DUF4152) / Nucleotidyltransferase; domain 5 / 2-Layer Sandwich / metal ion binding / Alpha Beta / DUF4152 domain-containing protein
Function and homology information
Biological speciesPyrococcus furiosus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.345 Å
AuthorsSu, J. / Liu, Z.-J.
CitationJournal: Protein Cell / Year: 2010
Title: Crystal structure of a novel non-Pfam protein PF2046 solved using low resolution B-factor sharpening and multi-crystal averaging methods
Authors: Su, J. / Li, Y. / Shaw, N. / Zhou, W.H. / Zhang, M. / Xu, H. / Wang, B.-C. / Liu, Z.-J.
History
DepositionDec 30, 2013Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 30, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 6, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Uncharacterized protein PF2046
B: Uncharacterized protein PF2046
C: Uncharacterized protein PF2046
D: Uncharacterized protein PF2046
E: Uncharacterized protein PF2046
F: Uncharacterized protein PF2046


Theoretical massNumber of molelcules
Total (without water)154,3576
Polymers154,3576
Non-polymers00
Water5,801322
1
A: Uncharacterized protein PF2046
B: Uncharacterized protein PF2046
E: Uncharacterized protein PF2046


Theoretical massNumber of molelcules
Total (without water)77,1793
Polymers77,1793
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4730 Å2
ΔGint-16 kcal/mol
Surface area28170 Å2
MethodPISA
2
C: Uncharacterized protein PF2046
D: Uncharacterized protein PF2046
F: Uncharacterized protein PF2046


Theoretical massNumber of molelcules
Total (without water)77,1793
Polymers77,1793
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4650 Å2
ΔGint-18 kcal/mol
Surface area28260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)218.381, 125.640, 94.044
Angle α, β, γ (deg.)90.00, 102.86, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
Uncharacterized protein PF2046


Mass: 25726.184 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus furiosus (archaea) / Strain: DSM 3638 / Gene: PF2046 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8TZE9
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 322 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 4.07 Å3/Da / Density % sol: 69.81 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 20% PEG 4000, 20% (v/v) 2-propanol, 0.1M sodium citrate, 0.1M sodium acetate pH 5.0, 0.1M sodium chloride, 10% (w/v) MPD, VAPOR DIFFUSION, HANGING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 0.9794 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: May 1, 2009
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 2.345→50 Å / Num. all: 103609 / Num. obs: 88068 / % possible obs: 85 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Biso Wilson estimate: 36.82 Å2
Reflection shellResolution: 2.34→2.4 Å / % possible all: 85

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Processing

Software
NameVersionClassification
HKL-2000data collection
SHARPphasing
PHENIX(phenix.refine: 1.8.2_1309)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 2.345→36.068 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.7905 / SU ML: 0.29 / σ(F): 1.35 / Phase error: 27.84 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2378 1999 2.27 %RANDOM
Rwork0.2014 ---
all0.2032 103609 --
obs0.2022 88068 85.09 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 155.09 Å2 / Biso mean: 52.4804 Å2 / Biso min: 21.49 Å2
Refinement stepCycle: LAST / Resolution: 2.345→36.068 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10542 0 0 322 10864
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01110734
X-RAY DIFFRACTIONf_angle_d1.43914562
X-RAY DIFFRACTIONf_dihedral_angle_d16.543990
X-RAY DIFFRACTIONf_chiral_restr0.111662
X-RAY DIFFRACTIONf_plane_restr0.0071854
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.3452-2.40380.3647850.27963652373751
2.4038-2.46880.32751000.2484294439459
2.4688-2.54140.3251120.23174807491967
2.5414-2.62340.29621240.23755357548174
2.6234-2.71720.24281360.25295854599082
2.7172-2.82590.29451520.24266521667390
2.8259-2.95450.27891610.23596959712096
2.9545-3.11020.24651670.234971807347100
3.1102-3.30490.28531680.230272287396100
3.3049-3.55990.25331670.2172037370100
3.5599-3.91770.26981210.18855192531371
3.9177-4.48370.18271680.158672317399100
4.4837-5.64550.17931670.152172377404100
5.6455-36.07210.211710.202573547525100
Refinement TLS params.Method: refined / Origin x: -36.3957 Å / Origin y: -60.8628 Å / Origin z: -0.2437 Å
111213212223313233
T0.2187 Å2-0.0004 Å2-0.001 Å2-0.2166 Å2-0.0017 Å2--0.2695 Å2
L0.308 °20.0054 °2-0.0311 °2-0.2684 °2-0.0016 °2--0.4044 °2
S-0.0115 Å °0.0144 Å °-0.0107 Å °-0.0224 Å °-0.0127 Å °-0.0028 Å °-0.0064 Å °0.0048 Å °0.0215 Å °
Refinement TLS groupSelection details: ALL

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