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- PDB-2dyy: Crystal structure of putative translation initiation inhibitor PH... -

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Basic information

Entry
Database: PDB / ID: 2dyy
TitleCrystal structure of putative translation initiation inhibitor PH0854 from Pyrococcus horikoshii
ComponentsUPF0076 protein PH0854
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / Putative translation initiation inhibitor / Pyrococcus horikoshii / trimer / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homology
Function and homology information


deaminase activity / cytosol
Similarity search - Function
RidA, conserved site / Uncharacterized protein family UPF0076 signature. / RidA family / RutC-like / YjgF/YER057c/UK114 family / Endoribonuclease L-PSP / RutC-like superfamily / 60s Ribosomal Protein L30; Chain: A; / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
RutC family protein PH0854
Similarity search - Component
Biological speciesPyrococcus horikoshii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsIhsanawati / Kishishita, S. / Murayama, K. / Chen, L. / Liu, Z.J. / Wang, B.C. / Shirouzu, M. / Bessho, Y. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: To be Published
Title: Crystal structure of putative translation initiation inhibitor PH0854 from Pyrococcus horikoshii
Authors: Ihsanawati / Kishishita, S. / Murayama, K. / Chen, L. / Liu, Z.J. / Wang, B.C. / Shirouzu, M. / Bessho, Y. / Yokoyama, S.
History
DepositionSep 19, 2006Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 19, 2007Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 25, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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: UPF0076 protein PH0854
B: UPF0076 protein PH0854
C: UPF0076 protein PH0854
D: UPF0076 protein PH0854
E: UPF0076 protein PH0854
F: UPF0076 protein PH0854
G: UPF0076 protein PH0854
H: UPF0076 protein PH0854
I: UPF0076 protein PH0854
J: UPF0076 protein PH0854
K: UPF0076 protein PH0854
L: UPF0076 protein PH0854


Theoretical massNumber of molelcules
Total (without water)168,62612
Polymers168,62612
Non-polymers00
Water4,197233
1
A: UPF0076 protein PH0854
B: UPF0076 protein PH0854
C: UPF0076 protein PH0854


Theoretical massNumber of molelcules
Total (without water)42,1573
Polymers42,1573
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5980 Å2
ΔGint-33 kcal/mol
Surface area14870 Å2
MethodPISA
2
D: UPF0076 protein PH0854
E: UPF0076 protein PH0854
F: UPF0076 protein PH0854


Theoretical massNumber of molelcules
Total (without water)42,1573
Polymers42,1573
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5600 Å2
ΔGint-29 kcal/mol
Surface area14210 Å2
MethodPISA
3
G: UPF0076 protein PH0854
H: UPF0076 protein PH0854
I: UPF0076 protein PH0854


Theoretical massNumber of molelcules
Total (without water)42,1573
Polymers42,1573
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5830 Å2
ΔGint-32 kcal/mol
Surface area14400 Å2
MethodPISA
4
J: UPF0076 protein PH0854
K: UPF0076 protein PH0854
L: UPF0076 protein PH0854


Theoretical massNumber of molelcules
Total (without water)42,1573
Polymers42,1573
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5850 Å2
ΔGint-36 kcal/mol
Surface area14560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.490, 43.090, 170.210
Angle α, β, γ (deg.)90.00, 91.51, 90.00
Int Tables number3
Space group name H-MP121

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Components

#1: Protein
UPF0076 protein PH0854 / Putative translation initiation inhibitor


Mass: 14052.204 Da / Num. of mol.: 12
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 / References: UniProt: O58584
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 233 / 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: 2.01 Å3/Da / Density % sol: 38.8 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 2M NaCl, 0.1M TrisHCl pH 7.0, 30% (w/v) PEG 3000, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 0.97914 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Nov 26, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97914 Å / Relative weight: 1
ReflectionResolution: 2.6→30 Å / Num. obs: 44546 / % possible obs: 96.6 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 39.2 Å2 / Rmerge(I) obs: 0.096
Reflection shellResolution: 2.6→2.76 Å / % possible all: 80.2

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1XRG

1xrg


Resolution: 2.6→29.73 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 1706561.8 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.295 2048 5 %RANDOM
Rwork0.209 ---
obs0.209 40877 96.7 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 43.6057 Å2 / ksol: 0.35284 e/Å3
Displacement parametersBiso mean: 42.1 Å2
Baniso -1Baniso -2Baniso -3
1--10.23 Å20 Å25.03 Å2
2--9.19 Å20 Å2
3---1.04 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.44 Å0.29 Å
Luzzati d res low-5 Å
Luzzati sigma a0.42 Å0.26 Å
Refinement stepCycle: LAST / Resolution: 2.6→29.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11228 0 0 233 11461
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d24.5
X-RAY DIFFRACTIONc_improper_angle_d0.8
LS refinement shellResolution: 2.6→2.76 Å / Rfactor Rfree error: 0.021 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.356 297 5.2 %
Rwork0.261 5444 -
obs--82.7 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top

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