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- PDB-3icx: Crystal structure of Sulfolobus solfataricus Nop5 (135-380) -

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Basic information

Entry
Database: PDB / ID: 3icx
TitleCrystal structure of Sulfolobus solfataricus Nop5 (135-380)
ComponentsPre mRNA splicing protein
KeywordsRNA BINDING PROTEIN / C/D guide RNA / 2'-O-methylation / coiled-coil
Function / homology
Function and homology information


box C/D methylation guide snoRNP complex / snoRNA binding
Similarity search - Function
DNA polymerase; domain 1 - #460 / Nop domain / Helix hairpin bin / : / : / Archaeal Nop5/56-rel, N-terminal domain / Nucleolar protein Nop56/Nop58 / NOSIC / NOSIC (NUC001) domain / Nop domain ...DNA polymerase; domain 1 - #460 / Nop domain / Helix hairpin bin / : / : / Archaeal Nop5/56-rel, N-terminal domain / 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 / DNA polymerase; domain 1 / Helix Hairpins / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Pre mRNA splicing protein
Similarity search - Component
Biological speciesSulfolobus solfataricus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.1 Å
AuthorsYe, K.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2009
Title: Structural organization of box C/D RNA-guided RNA methyltransferase.
Authors: Ye, K. / Jia, R. / Lin, J. / Ju, M. / Peng, J. / Xu, A. / Zhang, L.
History
DepositionJul 19, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 25, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
Revision 1.3Sep 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
A: Pre mRNA splicing protein
B: Pre mRNA splicing protein
C: Pre mRNA splicing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,1518
Polymers86,6713
Non-polymers4805
Water00
1
A: Pre mRNA splicing protein
B: Pre mRNA splicing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,0695
Polymers57,7812
Non-polymers2883
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2920 Å2
ΔGint-21.8 kcal/mol
Surface area22770 Å2
MethodPISA
2
C: Pre mRNA splicing protein
hetero molecules

C: Pre mRNA splicing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,1656
Polymers57,7812
Non-polymers3844
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_557-x,y,-z+21
Buried area2910 Å2
ΔGint-20.6 kcal/mol
Surface area22610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)153.645, 122.126, 71.786
Angle α, β, γ (deg.)90.000, 107.670, 90.000
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: LYS / Beg label comp-ID: LYS / End auth comp-ID: PHE / End label comp-ID: PHE / Refine code: 2 / Auth seq-ID: 135 - 378 / Label seq-ID: 2 - 245

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB
3CC

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Components

#1: Protein Pre mRNA splicing protein


Mass: 28890.275 Da / Num. of mol.: 3 / Fragment: UNP residues 135-380
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sulfolobus solfataricus (archaea) / Gene: SSO0939 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)/RIL+ / References: UniProt: Q97ZH3
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4

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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: 3.7 Å3/Da / Density % sol: 66.78 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.7
Details: 0.8M (NH4)2SO4, 10 mM MgCl2, and 50mM Na cacodylate, pH 6.7, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BSRF / Beamline: 3W1A / Wavelength: 0.98 Å
DetectorType: MAR CCD 165 mm / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 3.1→50 Å / Num. obs: 22817 / % possible obs: 99.4 % / Redundancy: 3.9 % / Rmerge(I) obs: 0.149 / Net I/σ(I): 10.5
Reflection shellResolution: 3.1→3.21 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.475 / Mean I/σ(I) obs: 2.6 / % possible all: 99.1

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMAC5.2.0019refinement
PDB_EXTRACT3.005data extraction
MAR345CCDdata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2NNW

2nnw


Resolution: 3.1→20 Å / Cor.coef. Fo:Fc: 0.866 / Cor.coef. Fo:Fc free: 0.811 / Occupancy max: 1 / Occupancy min: 1 / SU B: 48.322 / SU ML: 0.389 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 12.127 / ESU R Free: 0.48 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.304 1169 5.1 %RANDOM
Rwork0.261 ---
obs0.263 22738 99.06 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 93.12 Å2 / Biso mean: 23.468 Å2 / Biso min: 6.47 Å2
Baniso -1Baniso -2Baniso -3
1-0.93 Å20 Å2-0.67 Å2
2---1.66 Å20 Å2
3---0.33 Å2
Refinement stepCycle: LAST / Resolution: 3.1→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5361 0 25 0 5386
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0225456
X-RAY DIFFRACTIONr_angle_refined_deg1.1541.9787347
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.6415669
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.25923.605258
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.167151026
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.2891554
X-RAY DIFFRACTIONr_chiral_restr0.0810.2834
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.024029
X-RAY DIFFRACTIONr_nbd_refined0.220.22613
X-RAY DIFFRACTIONr_nbtor_refined0.3050.23744
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1350.2185
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2420.288
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0390.26
X-RAY DIFFRACTIONr_mcbond_it0.3161.53448
X-RAY DIFFRACTIONr_mcangle_it0.54125370
X-RAY DIFFRACTIONr_scbond_it0.81832229
X-RAY DIFFRACTIONr_scangle_it1.4694.51977
Refine LS restraints NCS

Dom-ID: 1 / Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Auth asym-IDNumberTypeRms dev position (Å)Weight position
A900TIGHT POSITIONAL0.030.05
B900TIGHT POSITIONAL0.020.05
C900TIGHT POSITIONAL0.030.05
A887MEDIUM POSITIONAL0.390.5
B887MEDIUM POSITIONAL0.370.5
C887MEDIUM POSITIONAL0.340.5
A900TIGHT THERMAL0.040.5
B900TIGHT THERMAL0.030.5
C900TIGHT THERMAL0.030.5
A887MEDIUM THERMAL0.272
B887MEDIUM THERMAL0.262
C887MEDIUM THERMAL0.262
LS refinement shellResolution: 3.1→3.18 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.367 72 -
Rwork0.323 1498 -
all-1570 -
obs--94.64 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.69193.027-2.56627.0742-3.9052.925-0.02350.14210.0228-0.31310.18730.22330.2349-0.0678-0.16380.23480.0028-0.09730.19230.08050.19395.28047.089848.1223
24.47121.5454-0.95254.0705-1.17323.64260.00960.1012-0.333-0.40330.11250.86160.0947-0.5229-0.12210.0660.0277-0.0610.15480.06630.3263-10.1521-3.292654.129
35.2457-3.072-0.07354.7219-2.33873.3296-0.2073-0.1934-0.18980.28090.15210.7982-0.0626-0.43350.05520.0072-0.06950.08760.09580.06890.4241-16.9196-4.702758.9175
40.50510.30070.06611.3594-1.36531.8224-0.160.1608-0.0713-0.1078-0.0636-0.0272-0.0292-0.01260.22360.1660.0073-0.02120.1880.01710.22183.261118.498734.5337
57.16244.40495.65976.82567.887910.8973-0.82930.91470.966-0.7741-0.17311.217-0.7775-0.16751.00240.2582-0.0261-0.08390.13340.02310.1445-4.777328.23821.7804
62.13681.73930.20882.26920.53250.1744-0.0260.1582-0.391-0.16330.052-0.31610.12780.0477-0.0260.19880.0464-0.03810.20540.04030.256713.67154.6454.8738
73.0516-0.07811.03723.5114-1.20724.69290.0832-0.04750.11720.256-0.0137-0.291-0.09520.2069-0.06960.08740.03340.00420.1063-0.02630.246322.338420.650961.3867
80.61851.3243-0.26885.5317-1.74150.62110.1181-0.2311-0.13020.24890.19670.5098-0.1948-0.1102-0.31470.28310.01520.00790.14540.03640.172310.1847-5.74264.4979
96.02361.615-0.46732.9669-0.14731.4380.14770.0757-0.3388-0.20080.06830.22290.13990.1905-0.2160.19990.0335-0.0160.11530.03030.203119.2648-23.883863.3513
108.62231.8643-4.7623.0763-0.09346.41290.3188-0.9588-1.600300.0453-0.3256-0.00291.169-0.36410.14310.0094-0.11190.1990.00540.228928.7149-26.244872.6687
111.25840.32-0.37250.4916-1.28565.2505-0.0266-0.0525-0.02150.0453-0.0184-0.0998-0.21430.20420.0450.2253-0.00180.01420.2033-0.0370.1603-15.207950.700674.2475
122.5097-0.6622-1.26721.4105-1.52433.4355-0.0877-0.3989-0.11430.1708-0.0113-0.20060.27930.24790.0990.20790.0254-0.01830.1199-0.00310.1615-14.086642.015786.9339
132.88372.2482-1.21916.2628-2.80241.2759-0.0710.349-0.44350.11040.0688-0.3491-0.04430.00340.00220.1849-0.04460.01950.2839-0.08470.1198-4.759350.947854.5096
144.70312.84112.84273.03131.73473.8512-0.22960.2880.2893-0.0970.0494-0.1569-0.2412-0.01550.18020.1756-0.03880.00880.13750.01590.14733.929565.316155.6211
157.74392.68575.2984.4463.527110.661-0.44211.0205-0.2576-0.30670.4324-0.50750.11970.79330.00970.122-0.11390.16440.2074-0.05770.050711.329958.3749.0289
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A135 - 165
2X-RAY DIFFRACTION2A166 - 189
3X-RAY DIFFRACTION3A190 - 232
4X-RAY DIFFRACTION4A233 - 354
5X-RAY DIFFRACTION5A355 - 378
6X-RAY DIFFRACTION6B135 - 175
7X-RAY DIFFRACTION7B176 - 232
8X-RAY DIFFRACTION8B233 - 282
9X-RAY DIFFRACTION9B283 - 359
10X-RAY DIFFRACTION10B360 - 378
11X-RAY DIFFRACTION11C135 - 188
12X-RAY DIFFRACTION12C189 - 245
13X-RAY DIFFRACTION13C246 - 282
14X-RAY DIFFRACTION14C283 - 344
15X-RAY DIFFRACTION15C345 - 378

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