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- PDB-3paf: M. jannaschii L7Ae mutant -

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Basic information

Entry
Database: PDB / ID: 3paf
TitleM. jannaschii L7Ae mutant
Components50S ribosomal protein L7Ae
KeywordsRIBOSOMAL PROTEIN / RNA binding protein / alpha beta sandwich / methylation core protein / K-turn RNA binding / nucleolus
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
ACETATE ION / Large ribosomal subunit protein eL8
Similarity search - Component
Biological speciesMethanocaldococcus jannaschii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsBiswas, S. / Maxwell, E.S.
CitationJournal: To be Published
Title: Structure and stability of M.jannaschii L7Ae El9 KtoQ mutant
Authors: Biswas, S. / Gagnon, K.T. / Mattos, C. / Brown, B.A. / Maxwell, E.S.
History
DepositionOct 19, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 2, 2011Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.2Sep 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_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: 50S ribosomal protein L7Ae
B: 50S ribosomal protein L7Ae
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,7726
Polymers25,4622
Non-polymers3104
Water3,351186
1
A: 50S ribosomal protein L7Ae
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,9233
Polymers12,7311
Non-polymers1922
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: 50S ribosomal protein L7Ae
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,8493
Polymers12,7311
Non-polymers1182
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)43.443, 55.634, 103.039
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: 12730.829 Da / Num. of mol.: 2 / Mutation: L87V, E88S, V89R, A90P, K26Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanocaldococcus jannaschii (archaea)
Gene: rpl7ae, MJ1203 / Plasmid: Pet 28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 Rosetta DE3 / References: UniProt: P54066
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 186 / 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: 2.45 Å3/Da / Density % sol: 49.7 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 30% PEG 2000MME, 0.1M Sodium acetate, 0.2M Ammonium sulfate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 200 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 0.97 Å
DetectorType: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Aug 26, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 1.7→50 Å / Num. obs: 24624 / % possible obs: 88.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 5.9 % / Biso Wilson estimate: 19 Å2 / Rmerge(I) obs: 0.074 / Rsym value: 0.074 / Net I/σ(I): 26.4
Reflection shellResolution: 1.7→1.76 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.519 / Mean I/σ(I) obs: 2.2 / % possible all: 59.2

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Processing

Software
NameVersionClassification
SERGUIprogramdata 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: 1.7→24.249 Å / SU ML: 0.18 / σ(F): 1.35 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2085 1260 5.12 %5% reflections were set aside for Rfree calculations
Rwork0.1826 ---
obs0.1839 24624 87.77 %-
all-24624 --
Solvent computationShrinkage radii: 1.13 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 42.77 Å2 / ksol: 0.355 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-21.1435 Å2-0 Å2-0 Å2
2---11.3963 Å2-0 Å2
3----9.7472 Å2
Refinement stepCycle: LAST / Resolution: 1.7→24.249 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1777 0 18 186 1981
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0091830
X-RAY DIFFRACTIONf_angle_d1.182476
X-RAY DIFFRACTIONf_dihedral_angle_d14.575698
X-RAY DIFFRACTIONf_chiral_restr0.095294
X-RAY DIFFRACTIONf_plane_restr0.005320
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.7720.2931010.25231698X-RAY DIFFRACTION58
1.772-1.85260.23161010.22312002X-RAY DIFFRACTION69
1.8526-1.95020.23971320.19742307X-RAY DIFFRACTION80
1.9502-2.07230.25031480.20132568X-RAY DIFFRACTION88
2.0723-2.23230.22791650.19472777X-RAY DIFFRACTION96
2.2323-2.45670.25161510.1872918X-RAY DIFFRACTION99
2.4567-2.81170.24111520.19372963X-RAY DIFFRACTION100
2.8117-3.54070.22191430.1763010X-RAY DIFFRACTION100
3.5407-24.25140.15711670.16343121X-RAY DIFFRACTION100
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)
10.94230.4696-0.50292.3136-0.5870.92730.0425-0.05380.0510.6991-0.06390.1314-0.21960.0328-0.01590.302-0.00140.04030.1061-0.0120.1148-0.871120.306-20.2133
21.5786-1.2218-0.55641.46010.29561.9620.14810.04010.3726-0.176-0.0942-0.575-0.34310.1165-0.08290.2269-0.04140.12530.17850.04170.347317.101123.0252-43.3653
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A
2X-RAY DIFFRACTION2chain B

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