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- PDB-3o85: Giardia lamblia 15.5kD RNA binding protein -

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Basic information

Entry
Database: PDB / ID: 3o85
TitleGiardia lamblia 15.5kD RNA binding protein
ComponentsRibosomal protein L7Ae
KeywordsRIBOSOMAL PROTEIN / alpha beta sandwich fold / K-turn RNA binding protein / Kink turn RNA
Function / homology
Function and homology information


box C/D methylation guide snoRNP complex / precatalytic spliceosome / U4/U6 x U5 tri-snRNP complex / maturation of LSU-rRNA / maturation of SSU-rRNA / small-subunit processome / mRNA splicing, via spliceosome / ribosome / RNA binding
Similarity search - Function
H/ACA ribonucleoprotein complex, subunit Nhp2-like / Ribosomal protein L30/S12 / 60s Ribosomal Protein L30; Chain: A; / Ribosomal protein L7Ae conserved site / Ribosomal protein L7Ae signature. / Ribosomal protein L7Ae/L8/Nhp2 family / Ribosomal protein L7Ae/L30e/S12e/Gadd45 / Ribosomal protein L7Ae/L30e/S12e/Gadd45 family / 50S ribosomal protein L30e-like / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesGiardia lamblia (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.806 Å
AuthorsBiswas, S. / Maxwell, E.S.
CitationJournal: Biochemistry / Year: 2011
Title: Comparative analysis of the 15.5kD box C/D snoRNP core protein in the primitive eukaryote Giardia lamblia reveals unique structural and functional features.
Authors: Biswas, S. / Buhrman, G. / Gagnon, K. / Mattos, C. / Brown, B.A. / Maxwell, E.S.
History
DepositionAug 2, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 16, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 7, 2011Group: Database references
Revision 1.3Sep 6, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ribosomal protein L7Ae
B: Ribosomal protein L7Ae


Theoretical massNumber of molelcules
Total (without water)25,7362
Polymers25,7362
Non-polymers00
Water3,981221
1
A: Ribosomal protein L7Ae


Theoretical massNumber of molelcules
Total (without water)12,8681
Polymers12,8681
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Ribosomal protein L7Ae


Theoretical massNumber of molelcules
Total (without water)12,8681
Polymers12,8681
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)56.876, 40.611, 59.937
Angle α, β, γ (deg.)90.00, 100.93, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Ribosomal protein L7Ae


Mass: 12867.991 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Giardia lamblia (eukaryote) / Strain: ATCC 50803 / Gene: GL50803_11287 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21DE3 Rosetta cells / References: UniProt: A8BMJ0
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 221 / 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: 53.63 %
Crystal growMethod: vapor diffusion / pH: 4.6
Details: 0.2M Ammonium sulphate, 25%PEG 4000, Sodium acetate, pH 4.6, VAPOR DIFFUSION

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1 Å
DetectorType: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Aug 26, 2008
RadiationMonochromator: Si 220 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 23525 / % possible obs: 93.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Rmerge(I) obs: 0.085
Reflection shellResolution: 1.8→1.86 Å / Rmerge(I) obs: 0.362 / % possible all: 85.7

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
PHENIX(phenix.refine: 1.6.2_432)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1ZWZ

1zwz


Resolution: 1.806→32.845 Å / SU ML: 0.23 / σ(F): 1.34 / Phase error: 26.86 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.255 1206 5.13 %RANDOM
Rwork0.2357 ---
all-23525 --
obs-23525 94.26 %-
Solvent computationShrinkage radii: 0.77 Å / VDW probe radii: 0.9 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 51.457 Å2 / ksol: 0.439 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-0.977 Å20 Å24.7045 Å2
2---0.0506 Å2-0 Å2
3----0.9264 Å2
Refinement stepCycle: LAST / Resolution: 1.806→32.845 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1750 0 0 221 1971
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0051813
X-RAY DIFFRACTIONf_angle_d0.7812476
X-RAY DIFFRACTIONf_dihedral_angle_d14.777669
X-RAY DIFFRACTIONf_chiral_restr0.043309
X-RAY DIFFRACTIONf_plane_restr0.003324
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.806-1.87830.3115860.26192005X-RAY DIFFRACTION77
1.8783-1.96380.28091270.25132405X-RAY DIFFRACTION92
1.9638-2.06730.30181400.24212464X-RAY DIFFRACTION94
2.0673-2.19680.2481370.23592542X-RAY DIFFRACTION97
2.1968-2.36640.27481270.22512516X-RAY DIFFRACTION97
2.3664-2.60450.22491210.22642595X-RAY DIFFRACTION98
2.6045-2.98110.25091500.23772568X-RAY DIFFRACTION98
2.9811-3.7550.24571660.22722598X-RAY DIFFRACTION99
3.755-32.850.24981520.24062626X-RAY DIFFRACTION97
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)
12.1134-0.617-0.61013.26150.36291.01380.12390.1811-0.0178-0.083-0.17130.0076-0.0982-0.10330.0280.07290.0119-0.01530.0823-0.01130.0508-24.3545.8671-9.5382
21.713-0.1092-0.85511.87660.48752.80680.12210.1276-0.0104-0.07-0.1518-0.0985-0.0348-0.16640.03020.09910.02130.00530.07750.00160.0779-4.5112-2.2141-27.514
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A
2X-RAY DIFFRACTION2chain B

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