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- PDB-2apo: Crystal Structure of the Methanococcus jannaschii Cbf5 Nop10 Complex -

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Basic information

Entry
Database: PDB / ID: 2apo
TitleCrystal Structure of the Methanococcus jannaschii Cbf5 Nop10 Complex
Components
  • Probable tRNA pseudouridine synthase B
  • Ribosome biogenesis protein Nop10
KeywordsIsomerase/RNA binding protein / Protein-Protein complex / Box H/ACA / snoRNP / Pseudouridine synthase / RNA modification / Zinc ribbon / PUA domain / Isomerase-RNA binding protein COMPLEX
Function / homology
Function and homology information


tRNA pseudouridine55 synthase / rRNA pseudouridine synthesis / box H/ACA sno(s)RNA 3'-end processing / pseudouridine synthesis / snRNA pseudouridine synthesis / tRNA pseudouridine synthase activity / tRNA pseudouridine synthesis / mRNA pseudouridine synthesis / pseudouridine synthase activity / snoRNA binding ...tRNA pseudouridine55 synthase / rRNA pseudouridine synthesis / box H/ACA sno(s)RNA 3'-end processing / pseudouridine synthesis / snRNA pseudouridine synthesis / tRNA pseudouridine synthase activity / tRNA pseudouridine synthesis / mRNA pseudouridine synthesis / pseudouridine synthase activity / snoRNA binding / rRNA processing / ribonucleoprotein complex / RNA binding
Similarity search - Function
Alpha-Beta Plaits - #3190 / H/ACA ribonucleoprotein complex, subunit Nop10 / Probable tRNA pseudouridine synthase B, archaeal / H/ACA ribonucleoprotein complex subunit Nop10 , archaeal-type / tRNA pseudouridine synthase B family / Dyskerin-like / DKCLD (NUC011) domain / DKCLD (NUC011) domain / H/ACA ribonucleoprotein complex, subunit Nop10 / H/ACA ribonucleoprotein complex, subunit Nop10 superfamily ...Alpha-Beta Plaits - #3190 / H/ACA ribonucleoprotein complex, subunit Nop10 / Probable tRNA pseudouridine synthase B, archaeal / H/ACA ribonucleoprotein complex subunit Nop10 , archaeal-type / tRNA pseudouridine synthase B family / Dyskerin-like / DKCLD (NUC011) domain / DKCLD (NUC011) domain / H/ACA ribonucleoprotein complex, subunit Nop10 / H/ACA ribonucleoprotein complex, subunit Nop10 superfamily / Nucleolar RNA-binding protein, Nop10p family / tRNA pseudouridylate synthase B, C-terminal / tRNA pseudouridylate synthase B C-terminal domain / Pseudouridine synthase II, N-terminal / TruB family pseudouridylate synthase (N terminal domain) / Uncharacterised domain CHP00451 / PUA domain / PUA domain / Archaeosine Trna-guanine Transglycosylase; Chain: A, domain 4 / Pseudouridine synthase, catalytic domain superfamily / Putative RNA-binding Domain in PseudoUridine synthase and Archaeosine transglycosylase / PUA domain / PUA domain profile. / Rubrerythrin, domain 2 / PUA-like superfamily / Single Sheet / Roll / Alpha-Beta Plaits / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
: / Ribosome biogenesis protein Nop10 / Probable tRNA pseudouridine synthase B
Similarity search - Component
Biological speciesMethanocaldococcus jannaschii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.95 Å
AuthorsHamma, T. / Reichow, S.L. / Varani, G. / Ferre-D'Amare, A.R.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2005
Title: The Cbf5-Nop10 complex is a molecular bracket that organizes box H/ACA RNPs.
Authors: Hamma, T. / Reichow, S.L. / Varani, G. / Ferre-D'Amare, A.R.
History
DepositionAug 16, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 15, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Probable tRNA pseudouridine synthase B
B: Ribosome biogenesis protein Nop10
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,5675
Polymers48,4232
Non-polymers1443
Water3,153175
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2670 Å2
ΔGint-16 kcal/mol
Surface area17080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)118.289, 63.189, 67.896
Angle α, β, γ (deg.)90.00, 102.62, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-502-

K

21A-692-

HOH

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Components

#1: Protein Probable tRNA pseudouridine synthase B / tRNA pseudouridine 55 synthase / Psi55 synthase / tRNA-uridine isomerase / tRNA pseudouridylate synthase


Mass: 41087.637 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanocaldococcus jannaschii (archaea)
Gene: truB / Plasmid: pET16b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus(DE3)-RIL
References: UniProt: Q57612, Isomerases; Intramolecular transferases; Transferring other groups
#2: Protein Ribosome biogenesis protein Nop10


Mass: 7335.383 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanocaldococcus jannaschii (archaea)
Gene: NOP10 / Plasmid: pET16b / Production host: Escherichia coli (E. coli) / Strain (production host): B834(DE3) / References: UniProt: P81303
#3: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 175 / 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: 2.65 Å3/Da / Density % sol: 51.88 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 5.8
Details: 2-propanol, PEG 4000, sodium citrate, potassium chloride, pH 5.8, VAPOR DIFFUSION, SITTING DROP, temperature 295.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 0.957, 0.9798
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 10, 2005
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.9571
20.97981
ReflectionResolution: 1.95→50 Å / Num. all: 33829 / Num. obs: 35760 / % possible obs: 94.6 % / Observed criterion σ(F): 5.15 / Observed criterion σ(I): 26.5 / Biso Wilson estimate: 20 Å2
Reflection shellResolution: 1.95→2.02 Å / % possible all: 70.2

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data reduction
SCALEPACKdata scaling
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 1.95→49.17 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 2097768.11 / Data cutoff high rms absF: 2097768.11 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.23 3377 10 %RANDOM
Rwork0.202 ---
all0.23 33829 --
obs0.202 35760 94.4 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 63.0258 Å2 / ksol: 0.411424 e/Å3
Displacement parametersBiso mean: 37.9 Å2
Baniso -1Baniso -2Baniso -3
1--5.72 Å20 Å23.82 Å2
2--5.8 Å20 Å2
3----0.08 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.27 Å0.23 Å
Luzzati d res low-5 Å
Luzzati sigma a0.22 Å0.19 Å
Refinement stepCycle: LAST / Resolution: 1.95→49.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2841 0 3 175 3019
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d23.3
X-RAY DIFFRACTIONc_improper_angle_d0
X-RAY DIFFRACTIONc_mcbond_it3.051.5
X-RAY DIFFRACTIONc_mcangle_it3.972
X-RAY DIFFRACTIONc_scbond_it4.822
X-RAY DIFFRACTIONc_scangle_it6.632.5
LS refinement shellResolution: 1.95→2.07 Å / Rfactor Rfree error: 0.014 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.298 431 9.7 %
Rwork0.261 3998 -
obs--74.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3ion.paramion.top

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