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- PDB-3gqx: Pyrococcus Horikoshii NOP5 RNA Binding Domain from a twinned crys... -

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Basic information

Entry
Database: PDB / ID: 3gqx
TitlePyrococcus Horikoshii NOP5 RNA Binding Domain from a twinned crystal form
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 / MOLECULAR REPLACEMENT / molecular replacement / 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 1.2Nov 14, 2012Group: Other
Revision 1.3Jul 26, 2017Group: Data collection / Refinement description / Source and taxonomy
Category: diffrn_detector / entity_src_gen / software / Item: _diffrn_detector.detector
Revision 1.4Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim / 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_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _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
B: NOP5P PROTEIN
A: NOP5P PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,3435
Polymers37,9632
Non-polymers3813
Water2,450136
1
A: NOP5P PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,1082
Polymers18,9811
Non-polymers1271
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: NOP5P PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,2353
Polymers18,9811
Non-polymers2542
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
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 number76
Space group name H-MP41
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain B and (resseq 243:293 or resseq 310:370 )
21chain A and (resseq 243:293 or resseq 310:370 )

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11LEULEUALAALABA243 - 29322 - 72
12HISHISLYSLYSBA310 - 37089 - 149
21LEULEUALAALAAB243 - 29322 - 72
22HISHISLYSLYSAB310 - 37089 - 149

NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(-0.004712, -0.99998, -0.003427), (-0.999885, 0.004662, 0.014445), (-0.014429, -0.003495, -0.99989)36.847301, 36.700199, 0.360842

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Components

#1: Protein NOP5P PROTEIN


Mass: 18981.275 Da / Num. of mol.: 2 / Fragment: RNA BINDING DOMAIN (UNP residues 244-391)
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.: 3 / Source method: obtained synthetically / Formula: I
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 136 / 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

Crystal
IDDensity Matthews (Å3/Da)Density % sol (%)
14.5569.87
2469.6
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
Reflection twinOperator: h,-k,-l / Fraction: 0.5
ReflectionResolution: 1.957→23.682 Å / Num. obs: 20529 / % possible obs: 84 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 11.7 % / Rsym value: 0.168

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 39.7
Highest resolutionLowest resolution
Rotation2.5 Å23.28 Å
Translation2.5 Å23.28 Å

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALA3.3.6data scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACT3.006data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3GQU

3gqu


Resolution: 2.5→23.682 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.738 / Cross valid method: THROUGHOUT / σ(F): 0.03 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflectionSelection details
Rfree0.287 1107 5.62 %RANDOM
Rwork0.252 ---
obs0.254 19699 93.48 %-
all-19699 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 119.326 Å2 / ksol: 0.384 e/Å3
Displacement parametersBiso max: 201.33 Å2 / Biso mean: 67.91 Å2 / Biso min: 10.22 Å2
Baniso -1Baniso -2Baniso -3
1--7.316 Å2-0 Å20 Å2
2---7.316 Å20 Å2
3---14.631 Å2
Refinement stepCycle: LAST / Resolution: 2.5→23.682 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1588 0 3 136 1727
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0041614
X-RAY DIFFRACTIONf_angle_d0.8652199
X-RAY DIFFRACTIONf_chiral_restr0.072256
X-RAY DIFFRACTIONf_plane_restr0.002285
X-RAY DIFFRACTIONf_dihedral_angle_d17.045523
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11B784X-RAY DIFFRACTIONPOSITIONAL
12A784X-RAY DIFFRACTIONPOSITIONAL0.025
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10 / % reflection obs: 98 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.5-2.5890.367950.33916341729
2.589-2.6930.407950.32517171812
2.693-2.8150.3871100.34417621872
2.815-2.9630.364940.30418041898
2.963-3.1490.2961050.29118751980
3.149-3.3910.291070.26419122019
3.391-3.7310.2481140.25219632077
3.731-4.2680.2681060.20919732079
4.268-5.3670.2351160.21719682084
5.367-23.6840.31210.25420282149

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