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- PDB-1xbi: High resolution structure of Methanocaldococcus jannaschii L7AE -

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Basic information

Entry
Database: PDB / ID: 1xbi
TitleHigh resolution structure of Methanocaldococcus jannaschii L7AE
Components50S ribosomal protein L7Ae
KeywordsRNA BINDING PROTEIN/STRUCTURAL PROTEIN / ALPHA-BETA-ALPHA SANDWICH FOLD / RNA BINDING PROTEIN-STRUCTURAL PROTEIN COMPLEX
Function / homology
Function and homology information


box C/D sno(s)RNA binding / ribonuclease P activity / tRNA 5'-leader removal / box C/D methylation guide snoRNP complex / box C/D snoRNP assembly / maturation of LSU-rRNA / maturation of SSU-rRNA / small-subunit processome / mRNA splicing, via spliceosome / cytosolic large ribosomal subunit ...box C/D sno(s)RNA binding / ribonuclease P activity / tRNA 5'-leader removal / box C/D methylation guide snoRNP complex / box C/D snoRNP assembly / maturation of LSU-rRNA / maturation of SSU-rRNA / small-subunit processome / mRNA splicing, via spliceosome / cytosolic large ribosomal subunit / rRNA binding / structural constituent of ribosome / translation
Similarity search - Function
Ribosomal protein L7Ae, archaea / 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
Large ribosomal subunit protein eL8
Similarity search - Component
Biological speciesMethanocaldococcus jannaschii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.45 Å
AuthorsBrown II, B.A. / Suryadi, J. / Lieberman, D.V. / Tran, E.J. / Maxwell, E.S.
CitationJournal: Biochemistry / Year: 2005
Title: The Crystal Structure of the Methanocaldococcus jannaschii Multifunctional L7Ae RNA-Binding Protein Reveals an Induced-Fit Interaction with the Box C/D RNAs.
Authors: Suryadi, J. / Tran, E.J. / Maxwell, E.S. / Brown II, B.A.
History
DepositionAug 30, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 9, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Aug 23, 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_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

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Assembly

Deposited unit
A: 50S ribosomal protein L7Ae
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,2242
Polymers12,9861
Non-polymers2381
Water3,117173
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)43.665, 48.869, 51.914
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein 50S ribosomal protein L7Ae


Mass: 12986.119 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanocaldococcus jannaschii (archaea)
Gene: RPL7AE, MJ1203 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta(DE3)pLysS (NOVAGEN) / References: UniProt: P54066
#2: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 173 / 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: 2.14 Å3/Da / Density % sol: 42.41 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 20% PEG 3350, 50mM HEPES, 10% isopropanol, 5% ethylene glycol, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X26C / Wavelength: 0.9 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jul 11, 2003
RadiationMonochromator: Si 111 crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.44→27.58 Å / Num. all: 21176 / Num. obs: 19412 / % possible obs: 100 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 7.1 % / Biso Wilson estimate: 19.8 Å2 / Rsym value: 0.079 / Net I/σ(I): 31.5044
Reflection shellResolution: 1.44→1.488 Å / Redundancy: 7 % / Mean I/σ(I) obs: 3.195 / Num. unique all: 1249 / Rsym value: 0.839 / % possible all: 70.4

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Processing

Software
NameVersionClassification
REFMAC5.2.0001refinement
MADNESSdata reduction
SCALEPACKdata scaling
EPMRphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1RA4

1ra4


Resolution: 1.45→27.63 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.954 / SU B: 2.524 / SU ML: 0.045 / Isotropic thermal model: Anisotropic / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 2 / ESU R: 0.074 / ESU R Free: 0.072 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19296 962 5 %RANDOM
Rwork0.13225 ---
all0.184 22372 --
obs0.13533 18451 95.64 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 14.082 Å2
Baniso -1Baniso -2Baniso -3
1--0.02 Å20 Å20 Å2
2--0.15 Å20 Å2
3----0.13 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.18 Å0.15 Å
Luzzati d res low-1.44 Å
Luzzati sigma a0.14 Å0.09 Å
Refinement stepCycle: LAST / Resolution: 1.45→27.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms958 0 15 173 1146
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0630.022983
X-RAY DIFFRACTIONr_bond_other_d0.0020.02968
X-RAY DIFFRACTIONr_angle_refined_deg4.592.0061326
X-RAY DIFFRACTIONr_angle_other_deg2.2432291
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5125117
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.25627.38142
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.04615208
X-RAY DIFFRACTIONr_dihedral_angle_4_deg34.465152
X-RAY DIFFRACTIONr_chiral_restr0.2730.2160
X-RAY DIFFRACTIONr_gen_planes_refined0.020.021020
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02146
X-RAY DIFFRACTIONr_nbd_refined0.2910.2203
X-RAY DIFFRACTIONr_nbd_other0.2320.2963
X-RAY DIFFRACTIONr_nbtor_other0.1240.2694
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2850.295
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3820.227
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3680.247
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.4650.226
X-RAY DIFFRACTIONr_mcbond_it4.1851.5747
X-RAY DIFFRACTIONr_mcbond_other1.5031.5240
X-RAY DIFFRACTIONr_mcangle_it4.5862978
X-RAY DIFFRACTIONr_scbond_it8.9743431
X-RAY DIFFRACTIONr_scangle_it11.5914.5348
X-RAY DIFFRACTIONr_rigid_bond_restr4.22132189
X-RAY DIFFRACTIONr_sphericity_free22.3685173
X-RAY DIFFRACTIONr_sphericity_bonded6.00951941
LS refinement shellResolution: 1.45→1.488 Å / Total num. of bins used: 20
RfactorNum. reflection
Rfree0.247 57
Rwork0.131 1249
obs-1249

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