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- PDB-7b8v: Circular permutant of ribosomal protein S6, P54-55 -

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Basic information

Entry
Database: PDB / ID: 7b8v
TitleCircular permutant of ribosomal protein S6, P54-55
Components30S ribosomal protein S6
KeywordsRIBOSOMAL PROTEIN / Circular permutant / native stacking / / designed amyloid fibril
Function / homology
Function and homology information


small ribosomal subunit rRNA binding / cytosolic small ribosomal subunit / structural constituent of ribosome / translation
Similarity search - Function
Ribosomal protein S6, conserved site / Ribosomal protein S6 signature. / Ribosomal protein S6, plastid/chloroplast / Ribosomal protein S6 / Ribosomal protein S6 / Ribosomal protein S6 superfamily / Translation elongation factor EF1B/ribosomal protein S6
Similarity search - Domain/homology
Small ribosomal subunit protein bS6
Similarity search - Component
Biological speciesThermus thermophilus HB27 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.863 Å
AuthorsWang, H. / Logan, D.T. / Oliveberg, M.
Funding support Sweden, 1items
OrganizationGrant numberCountry
Swedish Research Council Sweden
CitationJournal: To Be Published
Title: Circular permutant of ribosomal protein S6, P54-55
Authors: Wang, H. / Logan, D.T. / Oliveberg, M.
History
DepositionDec 13, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 12, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 30S ribosomal protein S6
S: 30S ribosomal protein S6
T: 30S ribosomal protein S6
W: 30S ribosomal protein S6
X: 30S ribosomal protein S6
U: 30S ribosomal protein S6
B: 30S ribosomal protein S6
C: 30S ribosomal protein S6
D: 30S ribosomal protein S6
E: 30S ribosomal protein S6
F: 30S ribosomal protein S6
G: 30S ribosomal protein S6
H: 30S ribosomal protein S6
I: 30S ribosomal protein S6
J: 30S ribosomal protein S6
K: 30S ribosomal protein S6
L: 30S ribosomal protein S6
M: 30S ribosomal protein S6
N: 30S ribosomal protein S6
O: 30S ribosomal protein S6
P: 30S ribosomal protein S6
Q: 30S ribosomal protein S6
R: 30S ribosomal protein S6
V: 30S ribosomal protein S6


Theoretical massNumber of molelcules
Total (without water)267,06524
Polymers267,06524
Non-polymers00
Water1,78399
1
A: 30S ribosomal protein S6
B: 30S ribosomal protein S6
D: 30S ribosomal protein S6
F: 30S ribosomal protein S6
G: 30S ribosomal protein S6
I: 30S ribosomal protein S6


Theoretical massNumber of molelcules
Total (without water)66,7666
Polymers66,7666
Non-polymers00
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
S: 30S ribosomal protein S6
T: 30S ribosomal protein S6
W: 30S ribosomal protein S6
X: 30S ribosomal protein S6
U: 30S ribosomal protein S6
O: 30S ribosomal protein S6


Theoretical massNumber of molelcules
Total (without water)66,7666
Polymers66,7666
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: 30S ribosomal protein S6
E: 30S ribosomal protein S6
H: 30S ribosomal protein S6
J: 30S ribosomal protein S6
K: 30S ribosomal protein S6
L: 30S ribosomal protein S6


Theoretical massNumber of molelcules
Total (without water)66,7666
Polymers66,7666
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
M: 30S ribosomal protein S6
N: 30S ribosomal protein S6
P: 30S ribosomal protein S6
Q: 30S ribosomal protein S6
R: 30S ribosomal protein S6
V: 30S ribosomal protein S6


Theoretical massNumber of molelcules
Total (without water)66,7666
Polymers66,7666
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)73.450, 73.630, 131.008
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number1
Space group name H-MP1

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Components

#1: Protein ...
30S ribosomal protein S6


Mass: 11127.690 Da / Num. of mol.: 24
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus HB27 (bacteria) / Gene: rpsF, rps6, TT_C1740 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: P62666
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 99 / 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: 53.64 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.2 M sodium bromide 0.1 M Bis-Tris propane pH 6.5 20% w/v PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.97625 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Sep 17, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.167
11h,-k,-l20.167
11-H, K, -L30.167
11-h,-k,l40.167
11K, H, -L50.083
11k,-h,l60.083
11-K, H, L70.083
11-K, -H, -L80.083
ReflectionResolution: 1.85→48.94 Å / Num. obs: 147738 / % possible obs: 93.8 % / Redundancy: 5.2 % / CC1/2: 0.994 / Rmerge(I) obs: 0.113 / Rpim(I) all: 0.055 / Rrim(I) all: 0.126 / Net I/σ(I): 8.6
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.863-2.0714.40.793865119470.4640.4040.8931.779.3
6.003-48.944.90.051957119450.9990.0260.0582198.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
Aimlessdata scaling
PDB_EXTRACT3.27data extraction
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1ris

1ris


Resolution: 1.863→48.94 Å / Cor.coef. Fo:Fc: 0.898 / Cor.coef. Fo:Fc free: 0.852 / SU B: 4.162 / SU ML: 0.131 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.055 / ESU R Free: 0.046 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2862 7073 4.8 %RANDOM
Rwork0.2468 ---
obs0.2487 140663 62.61 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 155.55 Å2 / Biso mean: 37.145 Å2 / Biso min: 10.46 Å2
Baniso -1Baniso -2Baniso -3
1-6.18 Å20.29 Å22.48 Å2
2---1.09 Å2-4.23 Å2
3----5.1 Å2
Refinement stepCycle: final / Resolution: 1.863→48.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16848 0 0 99 16947
Biso mean---26.07 -
Num. residues----2040
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.01317064
X-RAY DIFFRACTIONr_bond_other_d0.0010.01716296
X-RAY DIFFRACTIONr_angle_refined_deg1.5131.65123064
X-RAY DIFFRACTIONr_angle_other_deg1.091.57737488
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.16252016
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.97220.981224
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.753153168
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.16215240
X-RAY DIFFRACTIONr_chiral_restr0.0570.22088
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0219200
X-RAY DIFFRACTIONr_gen_planes_other0.0010.023792
LS refinement shellResolution: 1.863→1.894 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.334 32 -
Rwork0.131 412 -
obs--2.53 %

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