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- PDB-3n4z: Crystal structure of quintuple Arg-to-Lys variant of T. celer L30e -

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Basic information

Entry
Database: PDB / ID: 3n4z
TitleCrystal structure of quintuple Arg-to-Lys variant of T. celer L30e
Components50S ribosomal protein L30eRibosome
KeywordsRIBOSOMAL PROTEIN / L30e / quintuple / Arg-to-Lys
Function / homology
Function and homology information


cytosolic large ribosomal subunit / structural constituent of ribosome / translation / RNA binding
Similarity search - Function
Ribosomal protein L30/S12 / Ribosomal protein L30e / Ribosomal protein L30e, conserved site / Ribosomal protein L30/YlxQ / 60s Ribosomal Protein L30; Chain: A; / Ribosomal protein L30e signature 1. / Ribosomal protein L30e signature 2. / Ribosomal protein L7Ae/L30e/S12e/Gadd45 / Ribosomal protein L7Ae/L30e/S12e/Gadd45 family / 50S ribosomal protein L30e-like ...Ribosomal protein L30/S12 / Ribosomal protein L30e / Ribosomal protein L30e, conserved site / Ribosomal protein L30/YlxQ / 60s Ribosomal Protein L30; Chain: A; / Ribosomal protein L30e signature 1. / Ribosomal protein L30e signature 2. / 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 eL30
Similarity search - Component
Biological speciesThermococcus celer (archaea)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.3973 Å
AuthorsChan, C.H. / Wong, K.B.
CitationJournal: Plos One / Year: 2012
Title: Electrostatic contribution of surface charge residues to the stability of a thermophilic protein: benchmarking experimental and predicted pKa values
Authors: Chan, C.H. / Wilbanks, C.C. / Makhatadze, G.I. / Wong, K.B.
History
DepositionMay 24, 2010Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 9, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 1, 2012Group: Database references
Revision 1.3Jun 27, 2012Group: Database references
Revision 1.4Nov 1, 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 50S ribosomal protein L30e
B: 50S ribosomal protein L30e


Theoretical massNumber of molelcules
Total (without water)21,6832
Polymers21,6832
Non-polymers00
Water2,054114
1
A: 50S ribosomal protein L30e


Theoretical massNumber of molelcules
Total (without water)10,8421
Polymers10,8421
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: 50S ribosomal protein L30e


Theoretical massNumber of molelcules
Total (without water)10,8421
Polymers10,8421
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)30.487, 61.360, 102.767
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP22121

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Components

#1: Protein 50S ribosomal protein L30e / Ribosome


Mass: 10841.639 Da / Num. of mol.: 2 / Mutation: R8K, R21K, R42K, R54K, R76K
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermococcus celer (archaea) / Plasmid: pET3C / Production host: Escherichia coli (E. coli) / Strain (production host): C41 / References: UniProt: P29160
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 114 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.22 Å3/Da / Density % sol: 44.51 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.8M potassium phosphate, 0.8M sodium phosphate, 0.1M HEPES, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11101
21101
Diffraction source
SourceTypeIDWavelength (Å)
ROTATING ANODERIGAKU MICROMAX-00711.5418
ROTATING ANODERIGAKU MICROMAX-00721.5418
Detector
TypeIDDetectorDate
RIGAKU RAXIS IV1IMAGE PLATEJan 20, 2009
RIGAKU RAXIS IV2IMAGE PLATEJan 22, 2009
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Si 111 CHANNELSINGLE WAVELENGTHMx-ray1
2Si 111 CHANNELSINGLE WAVELENGTHMx-ray1
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.3973→39.44 Å / Num. obs: 8086 / % possible obs: 100 % / Observed criterion σ(F): 5 / Observed criterion σ(I): 5 / Redundancy: 14.7 % / Biso Wilson estimate: 33.97 Å2 / Rmerge(I) obs: 0.126 / Net I/σ(I): 15.4 / Num. measured all: 119186
Reflection shellResolution: 2.3973→2.53 Å / Redundancy: 14.7 % / Rmerge(I) obs: 0.268 / Mean I/σ(I) obs: 8.7 / Num. unique all: 16877 / % possible all: 100

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Processing

Software
NameVersionClassification
CrystalCleardata collection
MOLREPphasing
PHENIX(phenix.refine)refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1H7M

1h7m


Resolution: 2.3973→19.489 Å / Occupancy max: 1 / Occupancy min: 0.5 / SU ML: 0.8 / Cross valid method: THROUGHOUT / σ(F): 1.88 / Phase error: 22.5 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2498 803 10 %RANDOM
Rwork0.1818 7229 --
obs0.1887 8032 99.85 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 82.83 Å2 / ksol: 0.415 e/Å3
Displacement parametersBiso max: 70.27 Å2 / Biso mean: 27.763 Å2 / Biso min: 12.97 Å2
Baniso -1Baniso -2Baniso -3
1--4.2838 Å2-0 Å20 Å2
2---3.0827 Å2-0 Å2
3---7.3665 Å2
Refinement stepCycle: LAST / Resolution: 2.3973→19.489 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1421 0 0 114 1535
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071449
X-RAY DIFFRACTIONf_angle_d1.0691960
X-RAY DIFFRACTIONf_dihedral_angle_d14.562518
X-RAY DIFFRACTIONf_chiral_restr0.067233
X-RAY DIFFRACTIONf_plane_restr0.003248
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3973-2.54720.25481320.18741188X-RAY DIFFRACTION99
2.5472-2.74330.26451300.18081168X-RAY DIFFRACTION100
2.7433-3.01850.27541300.1731174X-RAY DIFFRACTION100
3.0185-3.45320.26791340.16141196X-RAY DIFFRACTION100
3.4532-4.34270.20381340.14951221X-RAY DIFFRACTION100
4.3427-19.48970.22621430.18071282X-RAY DIFFRACTION100

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