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- PDB-2fc3: Crystal structure of the extremely thermostable Aeropyrum pernix ... -

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Basic information

Entry
Database: PDB / ID: 2fc3
TitleCrystal structure of the extremely thermostable Aeropyrum pernix L7Ae multifunctional protein
Components50S ribosomal protein L7AeRibosome
KeywordsRIBOSOME / RNA BINDING PROTEIN / alpha-beta-alpha sandwich
Function / homology
Function and homology information


ribonuclease P activity / tRNA 5'-leader removal / ribosome biogenesis / rRNA binding / ribosome / structural constituent of ribosome / translation / ribonucleoprotein complex / cytoplasm
Similarity search - Function
Ribosomal protein L7Ae, prokaryotes / 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 ...Ribosomal protein L7Ae, prokaryotes / 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
50S ribosomal protein L7Ae
Similarity search - Component
Biological speciesAeropyrum pernix (archaea)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.56 Å
AuthorsBrown II, B.A. / Suryadi, J. / Zhou, Z. / Gupton Jr., T.B. / Flowers, S.L.
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2013
Title: Structure of the Aeropyrum pernix L7Ae multifunctional protein and insight into its extreme thermostability.
Authors: Bhuiya, M.W. / Suryadi, J. / Zhou, Z. / Brown, B.A.
History
DepositionDec 11, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 28, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Sep 11, 2013Group: Database references
Revision 1.4Oct 18, 2017Group: Refinement description / Category: software
Revision 1.5Aug 30, 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

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Assembly

Deposited unit
A: 50S ribosomal protein L7Ae


Theoretical massNumber of molelcules
Total (without water)13,6281
Polymers13,6281
Non-polymers00
Water2,144119
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)35.054, 49.188, 65.048
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 / Ribosome


Mass: 13627.869 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aeropyrum pernix (archaea) / Gene: rpl7ae / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta(DE3) pLysS / References: UniProt: Q9YAX7
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 119 / 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: 2.06 Å3/Da / Density % sol: 40.18 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 20% PEG 4000, 10% Isopropanol, 100 mM HEPES-KOH, pH 7.5, 1 mM ZnCl2 mixed 1:2 with 500 microMolar L7Ae protein, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.54 Å
DetectorType: RIGAKU SATURN 92 / Detector: CCD / Date: Aug 6, 2004 / Details: Osmic Confocal Blue Max-Flux
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.54→65.05 Å / Num. all: 34157 / Num. obs: 13926 / % possible obs: 81.5 % / Observed criterion σ(I): 3 / Redundancy: 2.45 % / Biso Wilson estimate: 17.53 Å2 / Rmerge(I) obs: 0.025 / Net I/σ(I): 23.7
Reflection shellResolution: 1.54→1.6 Å / Redundancy: 1.08 % / Rmerge(I) obs: 0.289 / Mean I/σ(I) obs: 2.3 / Num. unique all: 1678 / % possible all: 15.8

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Phasing

Phasing MRRfactor: 0.463 / Cor.coef. Fo:Fc: 0.535
Highest resolutionLowest resolution
Translation4 Å50 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
EPMR2.5phasing
REFMACrefinement
PDB_EXTRACT1.701data extraction
CrystalClearV. 1.3.6 (MSC/RIGAKU)data reduction
CrystalClearV. 1.3.6 (MSC/RIGAKU)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1XBI

1xbi


Resolution: 1.56→32.44 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.933 / SU B: 3.913 / SU ML: 0.064 / Isotropic thermal model: ISOTROPIC OVERALL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 1 / ESU R: 0.157 / ESU R Free: 0.103 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.226 695 5.1 %RANDOM
Rwork0.174 ---
all0.177 13760 --
obs0.177 13737 99.08 %-
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: 15.807 Å2
Baniso -1Baniso -2Baniso -3
1-0.02 Å20 Å20 Å2
2---0.56 Å20 Å2
3---0.54 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.24 Å0.21 Å
Luzzati d res low-5 Å
Luzzati sigma a0.17 Å0.12 Å
Refinement stepCycle: LAST / Resolution: 1.56→32.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms957 0 0 119 1076
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.022970
X-RAY DIFFRACTIONr_bond_other_d0.0010.02689
X-RAY DIFFRACTIONr_angle_refined_deg1.4192.0121311
X-RAY DIFFRACTIONr_angle_other_deg0.92831693
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4825123
X-RAY DIFFRACTIONr_dihedral_angle_2_deg27.43924.05437
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.01615185
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.801158
X-RAY DIFFRACTIONr_chiral_restr0.0850.2156
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021049
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02171
X-RAY DIFFRACTIONr_nbd_refined0.210.2208
X-RAY DIFFRACTIONr_nbd_other0.1930.2739
X-RAY DIFFRACTIONr_nbtor_refined0.1710.2493
X-RAY DIFFRACTIONr_nbtor_other0.0820.2506
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1210.276
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.0490.25
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3630.229
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1180.29
X-RAY DIFFRACTIONr_mcbond_it1.5421.5808
X-RAY DIFFRACTIONr_mcbond_other0.4311.5249
X-RAY DIFFRACTIONr_mcangle_it1.82221007
X-RAY DIFFRACTIONr_scbond_it3.1613389
X-RAY DIFFRACTIONr_scangle_it4.6344.5304
X-RAY DIFFRACTIONr_rigid_bond_restr2.13231947
X-RAY DIFFRACTIONr_sphericity_free11.2865119
X-RAY DIFFRACTIONr_sphericity_bonded3.04251646
LS refinement shellResolution: 1.56→1.6 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.875 10 -
Rwork0.243 217 -
obs-227 93.42 %

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