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- PDB-5yh1: Member of s1p family of ribosomal proteins PF0399 DHH domain -

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Basic information

Entry
Database: PDB / ID: 5yh1
TitleMember of s1p family of ribosomal proteins PF0399 DHH domain
ComponentsMember of s1p family of ribosomal proteins
KeywordsRIBOSOMAL PROTEIN / PF0399 / DHH Domain
Function / homology
Function and homology information


heat shock protein binding / unfolded protein binding / nucleic acid binding / ribosome
Similarity search - Function
Heat shock protein DnaJ, cysteine-rich domain / Zinc finger CR-type profile. / Heat shock protein DnaJ, cysteine-rich domain superfamily / DHH phosphoesterase superfamily / RNA-binding domain, S1 / OB-fold nucleic acid binding domain, AA-tRNA synthetase-type / OB-fold nucleic acid binding domain / S1 domain profile. / Ribosomal protein S1-like RNA-binding domain / S1 RNA binding domain ...Heat shock protein DnaJ, cysteine-rich domain / Zinc finger CR-type profile. / Heat shock protein DnaJ, cysteine-rich domain superfamily / DHH phosphoesterase superfamily / RNA-binding domain, S1 / OB-fold nucleic acid binding domain, AA-tRNA synthetase-type / OB-fold nucleic acid binding domain / S1 domain profile. / Ribosomal protein S1-like RNA-binding domain / S1 RNA binding domain / S1 domain / Nucleic acid-binding, OB-fold
Similarity search - Domain/homology
: / Member of s1p family of ribosomal proteins
Similarity search - Component
Biological speciesPyrococcus furiosus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.18 Å
AuthorsSong, Y. / Liu, X.P.
Funding support China, 1items
OrganizationGrant numberCountry
the National Natural Science Foundation of China31371260 China
CitationJournal: To Be Published
Title: Member of s1p family of ribosomal proteins PF0399 DHH domain
Authors: Song, Y. / Liu, X.P.
History
DepositionSep 27, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 1, 2018Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Member of s1p family of ribosomal proteins
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,0966
Polymers50,6731
Non-polymers4235
Water2,864159
1
A: Member of s1p family of ribosomal proteins
hetero molecules

A: Member of s1p family of ribosomal proteins
hetero molecules

A: Member of s1p family of ribosomal proteins
hetero molecules


Theoretical massNumber of molelcules
Total (without water)153,28818
Polymers152,0183
Non-polymers1,27015
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-y+1,x-y,z1
crystal symmetry operation3_665-x+y+1,-x+1,z1
Buried area7310 Å2
ΔGint-43 kcal/mol
Surface area54510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)132.500, 132.500, 212.245
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number182
Space group name H-MP6322

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Components

#1: Protein Member of s1p family of ribosomal proteins


Mass: 50672.602 Da / Num. of mol.: 1 / Fragment: DHH domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1) (archaea)
Strain: ATCC 43587 / DSM 3638 / JCM 8422 / Vc1 / Gene: PF0399 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8U3Q7
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mn
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 159 / 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: 5.31 Å3/Da / Density % sol: 76.84 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 4% (V/V) PEG 400 100 mM Sodium acetate/ Acetic acid pH 5.5 2000 mM Lithium sulfate 100 mM Magnesium sulfate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NFPSS / Beamline: BL19U1 / Wavelength: 0.9785 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 7, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9785 Å / Relative weight: 1
ReflectionResolution: 2.18→50 Å / Num. obs: 56239 / % possible obs: 97 % / Redundancy: 33.6 % / Net I/σ(I): 15

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Processing

Software
NameVersionClassification
REFMAC5.7.0032refinement
Cootmodel building
AutoSolphasing
HKL-3000data processing
RefinementResolution: 2.18→25.25 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.944 / SU B: 3.23 / SU ML: 0.082 / Cross valid method: THROUGHOUT / ESU R: 0.143 / ESU R Free: 0.129 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.202 2583 5.1 %RANDOM
Rwork0.187 ---
obs0.187 48383 87.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 34.78 Å2
Baniso -1Baniso -2Baniso -3
1-0.02 Å20.02 Å20 Å2
2--0.02 Å20 Å2
3----0.08 Å2
Refinement stepCycle: LAST / Resolution: 2.18→25.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3503 0 25 159 3687
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0193607
X-RAY DIFFRACTIONr_bond_other_d0.0010.023501
X-RAY DIFFRACTIONr_angle_refined_deg1.131.9854869
X-RAY DIFFRACTIONr_angle_other_deg0.73238086
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.065438
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.76223.916166
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.85615609
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.2251522
X-RAY DIFFRACTIONr_chiral_restr0.0670.2529
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0213984
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02780
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.3813.2811755
X-RAY DIFFRACTIONr_mcbond_other1.3813.2811754
X-RAY DIFFRACTIONr_mcangle_it2.2374.9162192
X-RAY DIFFRACTIONr_mcangle_other2.2374.9162193
X-RAY DIFFRACTIONr_scbond_it2.1783.6161852
X-RAY DIFFRACTIONr_scbond_other2.1773.6161852
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.4985.2832678
X-RAY DIFFRACTIONr_long_range_B_refined5.17626.4984145
X-RAY DIFFRACTIONr_long_range_B_other5.17526.4984145
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.18→2.24 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.262 110 -
Rwork0.233 2180 -
obs--54.56 %

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