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- PDB-3t7z: Structure of Methanocaldococcus jannaschii Nop N-terminal domain -

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Basic information

Entry
Database: PDB / ID: 3t7z
TitleStructure of Methanocaldococcus jannaschii Nop N-terminal domain
ComponentsNucleolar protein Nop 56/58
KeywordsPROTEIN BINDING / alpha beta fold / RNP assembly and methylation / L7Ae / box C/D RNA
Function / homology
Function and homology information


box C/D methylation guide snoRNP complex / snoRNA binding
Similarity search - Function
: / Nop5, N-terminal domain / Nucleotidyltransferase; domain 5 - #220 / : / Helix hairpin bin domain superfamily / Nucleolar protein Nop56/Nop58 / NOSIC / NOSIC (NUC001) domain / Nop domain / Nop domain superfamily ...: / Nop5, N-terminal domain / Nucleotidyltransferase; domain 5 - #220 / : / Helix hairpin bin domain superfamily / Nucleolar protein Nop56/Nop58 / NOSIC / NOSIC (NUC001) domain / Nop domain / Nop domain superfamily / Nop, C-terminal domain / snoRNA binding domain, fibrillarin / Nop domain profile. / Nucleotidyltransferase; domain 5 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / Uncharacterized NOP5 family protein MJ0694
Similarity search - Component
Biological speciesMethanocaldococcus jannaschii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.7 Å
AuthorsBiswas, S. / Maxwell, S.
CitationJournal: J.Biol.Chem. / Year: 2012
Title: Structurally Conserved Nop56/58 N-terminal Domain Facilitates Archaeal Box C/D Ribonucleoprotein-guided Methyltransferase Activity.
Authors: Gagnon, K.T. / Biswas, S. / Zhang, X. / Brown, B.A. / Wollenzien, P. / Mattos, C. / Maxwell, E.S.
History
DepositionJul 31, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 11, 2012Provider: repository / Type: Initial release
Revision 1.1Jun 13, 2012Group: Database references
Revision 1.2Jul 25, 2012Group: Database references
Revision 1.3Feb 28, 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

Downloads & links

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Assembly

Deposited unit
A: Nucleolar protein Nop 56/58
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,3314
Polymers14,1571
Non-polymers1743
Water1,27971
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)45.695, 86.511, 129.387
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number22
Space group name H-MF222
Components on special symmetry positions
IDModelComponents
11A-124-

HOH

21A-173-

HOH

31A-181-

HOH

41A-191-

HOH

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Components

#1: Protein Nucleolar protein Nop 56/58 / Uncharacterized NOP5 family protein MJ0694


Mass: 14157.104 Da / Num. of mol.: 1 / Fragment: N-terminal domain (UNP residues 1-119)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanocaldococcus jannaschii (archaea)
Gene: MJ0694 / Production host: Escherichia coli (E. coli) / References: UniProt: Q58105
#2: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 71 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.26 Å3/Da / Density % sol: 45.53 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 18% PEG 8000, 0.1M Sodium cacodylate, 0.2M Zinc acetate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1.0, 0.97924
DetectorType: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Jun 20, 2010
RadiationMonochromator: Si 111 channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
111
20.979241
ReflectionResolution: 1.7→50 Å / Num. obs: 12790 / % possible obs: 89 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 5.8 % / Rmerge(I) obs: 0.073 / Rsym value: 0.073 / Net I/σ(I): 38.4
Reflection shellResolution: 1.7→1.73 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.376 / Mean I/σ(I) obs: 2.95 / Rsym value: 0.376 / % possible all: 38.3

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Processing

Software
NameVersionClassification
HKL-2000data collection
SOLVEphasing
PHENIX(phenix.refine: 1.6.2_432)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 1.7→35.958 Å / SU ML: 0.21 / σ(F): 0 / Phase error: 25.13 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.231 615 5.04 %random
Rwork0.2017 ---
all0.2032 ---
obs0.2032 12202 84.98 %-
Solvent computationShrinkage radii: 0.72 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 56.792 Å2 / ksol: 0.42 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--9.2164 Å20 Å20 Å2
2--3.9293 Å20 Å2
3---5.2871 Å2
Refinement stepCycle: LAST / Resolution: 1.7→35.958 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms961 0 11 71 1043
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0281009
X-RAY DIFFRACTIONf_angle_d2.1931363
X-RAY DIFFRACTIONf_dihedral_angle_d14.532368
X-RAY DIFFRACTIONf_chiral_restr0.169146
X-RAY DIFFRACTIONf_plane_restr0.013172
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.87110.285860.2441705X-RAY DIFFRACTION51
1.8711-2.14180.24411690.20973073X-RAY DIFFRACTION91
2.1418-2.69830.24711860.19743334X-RAY DIFFRACTION98
2.6983-35.96630.21671740.19823475X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: -15.9052 Å / Origin y: 8.9238 Å / Origin z: -17.5078 Å
111213212223313233
T0.1497 Å2-0.0005 Å20.0398 Å2-0.1322 Å20.0167 Å2--0.1264 Å2
L1.0212 °20.4403 °20.3064 °2-1.3981 °20.3057 °2--0.8377 °2
S0.0296 Å °0.0972 Å °0.1396 Å °0.079 Å °-0.0004 Å °0.1831 Å °-0.0916 Å °0.1542 Å °-0.0186 Å °
Refinement TLS groupSelection details: chain A

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