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- PDB-2jrr: Solution NMR Structure of Q5LLS5 from Silicibacter pomeroyi. Nort... -

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Basic information

Entry
Database: PDB / ID: 2jrr
TitleSolution NMR Structure of Q5LLS5 from Silicibacter pomeroyi. Northeast Structural Genomics Consortium target SiR90
ComponentsUncharacterized protein
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / solution NMR Structure / Protein / SiR90 / PSI-2 / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG
Function / homologyq5lls5 like domains / HSP40/DNAj peptide-binding domain / Zinc finger, CHCC-type / Zinc-finger domain / Sandwich / Mainly Beta / zf-CHCC domain-containing protein
Function and homology information
Biological speciesSilicibacter pomeroyi (bacteria)
MethodSOLUTION NMR / simulated annealing
AuthorsSwapna, G.V.T. / Tejero, R. / Jiang, M. / Cunningham, K. / Maglaqui, M. / Owens, L. / Liu, J. / Wang, H. / Acton, T.B. / Xiao, R. ...Swapna, G.V.T. / Tejero, R. / Jiang, M. / Cunningham, K. / Maglaqui, M. / Owens, L. / Liu, J. / Wang, H. / Acton, T.B. / Xiao, R. / Baran, M.C. / Rost, B. / Montelione, G.T. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published
Title: Solution NMR Structure of Q5LLS5 from Silicibacter pomeroyi.
Authors: Swapna, G.V.T. / Tejero, R. / Jiang, M. / Cunningham, K. / Maglaqui, M. / Owens, L. / Liu, J. / Wang, H. / Acton, T.B. / Xiao, R. / Baran, M.B. / Rost, B. / Montelione, G.T.
History
DepositionJun 28, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 17, 2007Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 19, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _pdbx_database_status.status_code_cs / _pdbx_nmr_software.name / _struct_ref_seq_dif.details
Revision 1.4Jun 14, 2023Group: Database references / Other / Category: database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data
Revision 1.5Dec 20, 2023Group: Data collection / Other
Category: chem_comp_atom / chem_comp_bond / pdbx_database_status
Item: _pdbx_database_status.deposit_site

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)7,5171
Polymers7,5171
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Uncharacterized protein


Mass: 7516.512 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Silicibacter pomeroyi (bacteria) / Strain: DSS-3, DSM 15171
Description: The protein is a monomer by gel filtration chromatography and static light scattering.
Gene: SP03846 / Plasmid details: Plasmid / Plasmid: pET21 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)MAGIC / References: UniProt: Q5LLS5

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
2112D 1H-15N HSQC
2212D 1H-13C HSQC
1322D 1H-15N HSQC
1422D 1H-13C HSQC
1523D CBCA(CO)NH
1623D HN(CA)CB
1723D HBHA(CO)NH
1823D HNHA
1923D (H)CCH-TOCSY
11023D 1H-15N NOESY
11123D 1H-13C NOESY
31232D 1H-15N HSQC

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Sample preparation

Details
Solution-IDContents
10.65 mM 5% 13C, 100% 15N SiR90, 10 mM Tris, 5 mM DTT, 100 mM NaCl, 95% H2O/5% D2O
20.65 mM [U-100% 13C; U-100% 15N] SiR90, 10 mM Tris, 5 mM DTT, 100 mM NaCl, 95% H2O/5% D2O
30.65 mM [U-100% 13C; U-100% 15N] SiR90, 10 mM Tris, 5 mM DTT, 100 mM NaCl, 100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.65 mMSiR905% 13C, 100% 15N1
10 mMTris1
5 mMDTT1
100 mMNaCl1
0.65 mMSiR90[U-100% 13C; U-100% 15N]2
10 mMTris2
5 mMDTT2
100 mMNaCl2
0.65 mMSiR90[U-100% 13C; U-100% 15N]3
10 mMTris3
5 mMDTT3
100 mMNaCl3
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
1100 6.5 ambient 293 K
2100 6.5 ambient 293 K
3100 6.5 ambient 293 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA6001
Varian INOVAVarianINOVA5002

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Processing

NMR software
NameVersionDeveloperClassification
PSVS1.3Bhattacharya , Hang and Montelionestructure validation
PdbStat4.1Roberto Tejero and Montelionedata analysis
CNS1.1Brunger, Adams, Clore, Gros, Nilges and Readrefinement
X-PLOR NIH2.11.2Schwieters, Kuszewski, Tjandra and Clorerefinement
AutoStructure2.1.1Huang, Tejero, Powers and Montelionerefinement
AutoStructure2.1.1Huang, Tejero, Powers and Montelionestructure solution
NMRPipe2.3Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
Sparky3.11Goddarddata analysis
VNMR6.1cVariancollection
AutoAssign2.2.1Zimmerman, Moseley, Kulikowski and Montelionechemical shift assignment
RefinementMethod: simulated annealing / Software ordinal: 1
Details: The structures are based on a total of 819 conformationally restricting NOE-derived distance constraints, 52 dihedral angle constraints, and 26 hydrogen bond constraints.(14.5 constraints ...Details: The structures are based on a total of 819 conformationally restricting NOE-derived distance constraints, 52 dihedral angle constraints, and 26 hydrogen bond constraints.(14.5 constraints per residue, 5.2 long-range constraints per residue, computed for residues 1-62 by PSVS 1.3). Residues 62-67 correspond to the Histidines of the C-terminal tag and could not be assigned. Structure determination was performed iteratively using AutoStructure (XPLOR-NIH). After a final XPLOR calculation using the constraints derived from AutoStructure, the 20 lowest energy structures out of 100 were further refined by restrained Molecular dynamics/Energy minimization in explicit water (CNS). The C-terminal HIS-tag residues of the protein were included in the calculations as well as the deposition. Coordinates for the following residues are not well determined: 1-7,18-29,46-48,58-67. The structure was determined using standard Triple resonance NMR experiments. Automated backbone assignments were made using AutoAssign and the sidechain assignments were completed manually. Automatic NOESY assignments as well as distance, dihedral angle and hydrogen-bond constraints were determined using AutoStructure. Structure quality factors, where ordered residues comprise: 8-17,30-45,49-57. RMSD of BB 0.5A, heavy atoms 1.0A. Ramachandran statistics for ordered residues: Most favoured: 91.1%, Additionally allowed: 8.9%, Generally allowed: 0.0%, Unfavourable: 0%. Procheck scores for ordered residues (raw/Z) phi-psi: -0.56/-1.89; all -0.33/-1.95. Molprobity clash score (raw/Z) 17.48/-1.47. RPF scores for goodness of fit to NOESY data: recall: 0.943, precision: 0.92, F-measure: 0.93. Final DP-score 0.795.
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20
NMR ensemble rmsDistance rms dev: 0.02 Å

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