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- PDB-2i0x: Hypothetical protein PF1117 from Pyrococcus furiosus -

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Basic information

Entry
Database: PDB / ID: 2i0x
TitleHypothetical protein PF1117 from Pyrococcus furiosus
ComponentsHypothetical protein PF1117Hypothesis
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / PF1117 / HYPOTHETICAL PROTEIN / PYROCOCCUS FURIOSUS / PSI / SOUTHEAST COLLABORATORY FOR STRUCTURAL GENOMICS / Protein Structure Initiative / SECSG
Function / homology
Function and homology information


maintenance of CRISPR repeat elements / RNA endonuclease activity / defense response to virus / Hydrolases; Acting on ester bonds / metal ion binding
Similarity search - Function
CRISPR-associated endonuclease Cas2 / Virulence-associated protein D / CRISPR associated protein Cas2 / CRISPR associated protein Cas2 / Alpha-Beta Plaits - #240 / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
CRISPR-associated endoribonuclease Cas2
Similarity search - Component
Biological speciesPyrococcus furiosus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.7 Å
AuthorsChen, L.Q. / Fu, Z.-Q. / Liu, Z.-J. / Rose, J.P. / Wang, B.C. / Southeast Collaboratory for Structural Genomics (SECSG)
CitationJournal: To be Published
Title: Crystal Structure of Hypothetical Protein Pf1117 from Pyrococcus furiosus
Authors: Chen, L.Q. / Fu, Z.-Q. / Hwang, J. / Chang, J. / Chen, L. / Wang, Y. / Zhang, H. / Liu, Z.-J. / Rose, J.P. / Wang, B.C. / Southeast Collaboratory for Structural Genomics
History
DepositionAug 11, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 10, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Sep 13, 2017Group: Refinement description / Category: refine / Item: _refine.pdbx_method_to_determine_struct
Revision 1.4Feb 21, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Hypothetical protein PF1117


Theoretical massNumber of molelcules
Total (without water)9,9931
Polymers9,9931
Non-polymers00
Water28816
1
A: Hypothetical protein PF1117

A: Hypothetical protein PF1117


Theoretical massNumber of molelcules
Total (without water)19,9852
Polymers19,9852
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_775-y+2,-x+2,-z+1/21
Buried area2910 Å2
ΔGint-18 kcal/mol
Surface area9130 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)48.203, 48.203, 84.272
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
DetailsPISA suggests that the biological assembly is a a2 dimer. The second part of the biological assembly can be generated by the following operator: -Y+2,-X+2,-z+0.5 symmetry ID 8_665

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Components

#1: Protein Hypothetical protein PF1117 / Hypothesis


Mass: 9992.677 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus furiosus (archaea) / Gene: ORF 1117 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: Q8U1T8
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 16 / 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: 2.45 Å3/Da / Density % sol: 49.77 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 4.2
Details: 1 MICROLITER DROPS CONTAINING EQUAL VOLUMES OF PROTEIN SOLUTION (10 MG/ML) AND A PRECIPITANT SOLUTION CONTAINING 20% PEG 8000, 200 MM SODIUM CHLORIDE, 12% GLYCEROL IN 100MM PHOSPHATE-CITRATE ...Details: 1 MICROLITER DROPS CONTAINING EQUAL VOLUMES OF PROTEIN SOLUTION (10 MG/ML) AND A PRECIPITANT SOLUTION CONTAINING 20% PEG 8000, 200 MM SODIUM CHLORIDE, 12% GLYCEROL IN 100MM PHOSPHATE-CITRATE BUFFER, pH 4.2, VAPOR DIFFUSION, SITTING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 0.9724 / Wavelength: 0.9724 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Mar 17, 2006 / 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: 2.4→50 Å / Num. obs: 4033 / % possible obs: 93.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 21.1 % / Rsym value: 0.056 / Net I/σ(I): 20.2
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 5.8 % / Mean I/σ(I) obs: 3.7 / Num. unique all: 239 / Rsym value: 0.295 / % possible all: 58.3

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Processing

Software
NameVersionClassification
SGXPROmodel building
CNS1.1refinement
SERGUIdata collection
HKL-2000data reduction
HKL-2000data scaling
SGXPROphasing
RefinementMethod to determine structure: SAD / Resolution: 2.7→25 Å / Data cutoff high rms absF: 10000 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.305 482 9.3 %RANDOM
Rwork0.261 ---
obs0.261 5038 96.7 %-
all-5210 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 46.0341 Å2 / ksol: 0.306465 e/Å3
Displacement parametersBiso mean: 58.2 Å2
Baniso -1Baniso -2Baniso -3
1--5.42 Å20 Å20 Å2
2---5.42 Å20 Å2
3---10.83 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.53 Å0.4 Å
Luzzati d res low-5 Å
Luzzati sigma a0.48 Å0.37 Å
Refinement stepCycle: LAST / Resolution: 2.7→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms693 0 0 16 709
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d23.1
X-RAY DIFFRACTIONc_improper_angle_d0.95
X-RAY DIFFRACTIONc_mcbond_it1.571.5
X-RAY DIFFRACTIONc_mcangle_it2.762
X-RAY DIFFRACTIONc_scbond_it2.042
X-RAY DIFFRACTIONc_scangle_it3.012.5
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP

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