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- PDB-3gqu: Pyrococcus Horikoshii NOP5 RNA Binding Domain -

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Basic information

Entry
Database: PDB / ID: 3gqu
TitlePyrococcus Horikoshii NOP5 RNA Binding Domain
ComponentsNOP5P PROTEIN
KeywordsRNA BINDING PROTEIN / RNA BINDING DOMAIN
Function / homology
Function and homology information


box C/D methylation guide snoRNP complex / snoRNA binding / small-subunit processome
Similarity search - Function
Nop domain / : / : / Archaeal Nop5/56-rel, N-terminal domain / Helix hairpin bin domain superfamily / Nucleolar protein Nop56/Nop58 / NOSIC / NOSIC (NUC001) domain / Nop domain / Nop domain superfamily ...Nop domain / : / : / Archaeal Nop5/56-rel, N-terminal domain / 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. / Serum Albumin; Chain A, Domain 1 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
IODIDE ION / Nop domain-containing protein
Similarity search - Component
Biological speciesPyrococcus horikoshii (archaea)
MethodX-RAY DIFFRACTION / SAD / Resolution: 2.5 Å
AuthorsReyes, F.E. / Hardin, J.W. / Batey, R.T.
CitationJournal: J.Biol.Chem. / Year: 2009
Title: Analysis of a Critical Interaction within the Archaeal Box C/D Small Ribonucleoprotein Complex
Authors: Hardin, J.W. / Reyes, F.E. / Batey, R.T.
History
DepositionMar 24, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 21, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jul 26, 2017Group: Data collection / Refinement description / Source and taxonomy
Category: diffrn_detector / entity_src_gen / software / Item: _diffrn_detector.detector
Revision 1.3Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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: NOP5P PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,50413
Polymers18,9811
Non-polymers1,52312
Water1,04558
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)73.604, 73.604, 114.279
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein NOP5P PROTEIN


Mass: 18981.275 Da / Num. of mol.: 1 / Fragment: RNA BINDING DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus horikoshii (archaea) / Gene: NOP5P, PH0053 / Plasmid: PET41B / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): ROSETTA BL21 (DE3) PLYSS / References: UniProt: O57810
#2: Chemical
ChemComp-IOD / IODIDE ION


Mass: 126.904 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: I
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 58 / 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: 4.55 Å3/Da / Density % sol: 69.87 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 6.8
Details: 500MM POTASSIUM IODIDE, 2% PEG 3350, pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 290K

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Data collection

DiffractionMean temperature: 93.15 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.502 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Nov 8, 2006
RadiationMonochromator: Ni FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.502 Å / Relative weight: 1
ReflectionResolution: 1.957→23.682 Å / Num. obs: 13956 / % possible obs: 84.7 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 21.8 % / Rsym value: 0.149 / Net I/σ(I): 4.944
Reflection shellResolution: 1.95→2.06 Å / Redundancy: 6.2 % / Rmerge(I) obs: 0.04 / Mean I/σ(I) obs: 0.2 / Num. measured all: 5530 / Num. unique all: 888 / Rsym value: 0.03971 / % possible all: 27

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Phasing

PhasingMethod: SAD
Phasing MADD res high: 1.96 Å / D res low: 23.68 Å / FOM : 0.284 / FOM acentric: 0.307 / FOM centric: 0.179 / Reflection: 19657 / Reflection acentric: 16159 / Reflection centric: 2922
Phasing dmFOM : 0.48 / FOM acentric: 0.47 / FOM centric: 0.51 / Reflection: 19704 / Reflection acentric: 16781 / Reflection centric: 2923
Phasing dm shell
Resolution (Å)FOM FOM acentricFOM centricReflectionReflection acentricReflection centric
5.6-23.6830.920.940.891109719390
3.5-5.60.90.920.831712526645
2.8-3.50.620.640.5239263312614
2.5-2.80.350.360.2838773361516
2.1-2.50.250.250.2361545496658
2-2.10.130.130.114671367100

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALA3.3.6data scaling
PHASERphasing
RESOLVE2.13phasing
PHENIXrefinement
PDB_EXTRACT3.006data extraction
RefinementMethod to determine structure: SAD / Resolution: 2.5→23.683 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.55 / σ(F): 1.58 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflectionSelection details
Rfree0.334 1142 10.01 %RANDOM
Rwork0.299 ---
obs0.302 11411 100 %-
all-11411 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 92.238 Å2 / ksol: 0.363 e/Å3
Displacement parametersBiso max: 169.84 Å2 / Biso mean: 50.012 Å2 / Biso min: 25.12 Å2
Baniso -1Baniso -2Baniso -3
1--5.998 Å20 Å20 Å2
2---5.998 Å20 Å2
3---11.996 Å2
Refinement stepCycle: LAST / Resolution: 2.5→23.683 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms811 0 12 58 881
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.011825
X-RAY DIFFRACTIONf_angle_d1.5971126
X-RAY DIFFRACTIONf_chiral_restr0.102132
X-RAY DIFFRACTIONf_plane_restr0.005146
X-RAY DIFFRACTIONf_dihedral_angle_d19.647268
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 8 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.5-2.6140.3931400.30112581398
2.614-2.7510.3561390.29112441383
2.751-2.9230.3531400.28312581398
2.923-3.1490.371400.28112591399
3.149-3.4650.3581410.27712731414
3.465-3.9640.2691420.24712801422
3.964-4.9860.2521460.23613121458
4.986-23.6840.3391540.31313851539

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