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- PDB-2jx5: Solution structure of the ubiquitin domain N-terminal to the S27a... -

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Basic information

Entry
Database: PDB / ID: 2jx5
TitleSolution structure of the ubiquitin domain N-terminal to the S27a ribosomal subunit of Giardia lamblia
ComponentsGlUb(S27a)
KeywordsRIBOSOMAL PROTEIN / ubiquitin / ribosome / recombination / GlUb / evolution
Function / homology
Function and homology information


ribosome / structural constituent of ribosome / ribonucleoprotein complex / translation
Similarity search - Function
Beta-grasp domain / S27a-like superfamily / Beta-grasp domain superfamily / Ribosomal protein S27a / Ribosomal protein S27a / Ribosomal protein S27a / Ubiquitin-like (UB roll) / Zinc-binding ribosomal protein / Roll / Alpha Beta
Similarity search - Domain/homology
Ribosomal protein S27a
Similarity search - Component
Biological speciesGiardia lamblia ATCC 50803 (eukaryote)
MethodSOLUTION NMR / simulated annealing
AuthorsCatic, A. / Sun, Z.J. / Ratner, D.M. / Misaghi, S. / Spooner, E. / Samuelson, J. / Wagner, G. / Ploegh, H.L.
CitationJournal: EMBO J. / Year: 2007
Title: Sequence and structure evolved separately in a ribosomal ubiquitin variant
Authors: Catic, A. / Sun, Z.J. / Ratner, D.M. / Misaghi, S. / Spooner, E. / Samuelson, J. / Wagner, G. / Ploegh, H.L.
History
DepositionNov 7, 2007Deposition site: BMRB / Processing site: RCSB
Revision 1.0Dec 4, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 16, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_spectrometer ...database_2 / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details
Revision 1.3May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: GlUb(S27a)


Theoretical massNumber of molelcules
Total (without water)7,3041
Polymers7,3041
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 50structures with the lowest energy
RepresentativeModel #1closest to the average

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Components

#1: Protein GlUb(S27a)


Mass: 7304.318 Da / Num. of mol.: 1 / Fragment: UNp residues 1-67
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Giardia lamblia ATCC 50803 (eukaryote) / Species: Giardia intestinalis / Strain: MR4
Description: contains GB1 domain at the N-terminus and 6-His tag at the C-terminus (both excluded from structure calculations)
Gene: S27a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / Variant (production host): BL21(DE3) / References: UniProt: A8BNY1

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
Details: Solution structure of ubiquitin domain N-terminal to S27a ribosome subunit from Giardia lamblia
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1213D HNCA
1313D HN(CA)CB
1413D HNCO
1513D C(CO)NH
1613D H(CCO)NH
1713D (H)CCH-TOCSY
1813D 1H-13C NOESY
1913D 1H-15N NOESY
11022D 1H-1H NOESY
11122D 1H-1H TOCSY
11232D 1H-13C HSQC

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Sample preparation

Details
Solution-IDContentsSolvent system
11 mM [U-99% 13C; U-99% 15N] GlUb(S27a), 10 mM potassium phosphate, 100 mM sodium chloride, 10 % D2O, 90% H2O/10% D2O90% H2O/10% D2O
21 mM GlUb(S27a), 10 mM potassium phosphate, 100 mM sodium chloride, 100% D2O100% D2O
31 mM [U-10% 13C] GlUb(S27a), 10 mM potassium phosphate, 100 mM sodium chloride, 100% D2O100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMGlUb(S27a)[U-99% 13C; U-99% 15N]1
10 mMpotassium phosphate1
100 mMsodium chloride1
10 %D2O1
1 mMGlUb(S27a)2
10 mMpotassium phosphate2
100 mMsodium chloride2
1 mMGlUb(S27a)[U-10% 13C]3
10 mMpotassium phosphate3
100 mMsodium chloride3
Sample conditionsIonic strength: 100 / pH: 6.2 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA6001
Bruker AvanceBrukerAVANCE7502
Varian INOVAVarianINOVA5003

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Processing

NMR software
NameVersionDeveloperClassification
PROSA3.7Guntertprocessing
CARA1.8.2Keller and Wuthrichdata analysis
RNMRTK3Stern and Hochprocessing
TALOS2003.027.13.05Cornilescu, Delaglio and Baxdata analysis
CYANA2.1Guntert, Mumenthaler and Wuthrichstructure solution
CYANA2.1Guntert, Mumenthaler and Wuthrichrefinement
RefinementMethod: simulated annealing / Software ordinal: 1
Details: default anneal macro with 10000 steps include 20 stereospecific ssignment for methyl groups
NMR constraintsNOE constraints total: 830 / NOE intraresidue total count: 487 / NOE long range total count: 101 / NOE medium range total count: 51 / NOE sequential total count: 191 / Protein chi angle constraints total count: 0 / Protein phi angle constraints total count: 42 / Protein psi angle constraints total count: 42
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 50 / Conformers submitted total number: 10 / Maximum torsion angle constraint violation: 5 ° / Maximum upper distance constraint violation: 0.5 Å

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