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- PDB-2k49: Solution NMR structure of UPF0339 protein SO3888 from Shewanella ... -

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Basic information

Entry
Database: PDB / ID: 2k49
TitleSolution NMR structure of UPF0339 protein SO3888 from Shewanella oneidensis. Northeast Structural Genomics Consortium target SoR190
ComponentsUPF0339 protein SO_3888
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / solution NMR structure / PSI-2 / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG
Function / homologyPH-domain like - #80 / Domain of unknown function DUF1508 / Domain of unknown function (DUF1508) / YegP-like superfamily / PH-domain like / Roll / Mainly Beta / UPF0339 protein SO_3888
Function and homology information
Biological speciesShewanella oneidensis (bacteria)
MethodSOLUTION NMR / simulated annealing
AuthorsTang, Y. / Wang, D. / Nwosu, C. / Maglaqui, M. / Xiao, R. / Liu, J. / Baran, M.C. / Swapna, G.V.T. / Acton, T.B. / Rost, B. ...Tang, Y. / Wang, D. / Nwosu, C. / Maglaqui, M. / Xiao, R. / Liu, J. / Baran, M.C. / Swapna, G.V.T. / Acton, T.B. / Rost, B. / Montelione, G.T. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published
Title: Solution NMR structure of UPF0339 protein SO3888 from Shewanella oneidensis.
Authors: Tang, Y. / Wang, D. / Nwosu, C. / Maglaqui, M. / Xiao, R. / Liu, J. / Baran, M.C. / Swapna, G.V.T. / Acton, T.B. / Rost, B. / Montelione, G.T.
History
DepositionMay 31, 2008Deposition site: BMRB / Processing site: RCSB
Revision 1.0Jul 8, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.2Feb 19, 2020Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer / struct_ref_seq_dif
Item: _pdbx_database_status.status_code_cs / _pdbx_nmr_software.name ..._pdbx_database_status.status_code_cs / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details
Revision 1.3Jun 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 1.4May 8, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: UPF0339 protein SO_3888


Theoretical massNumber of molelcules
Total (without water)13,1041
Polymers13,1041
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)20 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein UPF0339 protein SO_3888


Mass: 13103.619 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Shewanella oneidensis (bacteria) / Strain: MR-1 / Gene: SO_3888 / Plasmid: SoR190-21.2 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8EAL4

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1212D 1H-13C HSQC
1313D 1H-15N NOESY
1413D simutaneous NOESY
1513D 1H-13C NOESY aromatic
1613D HNCO
1713D HN(CA)CB
1813D CBCA(CO)NH
1913D (H)CCH-COSY
11013D (H)CCH-TOCSY
11113D HBHA(CO)NH
11222D 1H-13C HSQC high resolution
11313D CCH-TOCSY
NMR detailsText: The protein is a monomer by gel filtration chromatography and static light scattering.

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Sample preparation

Details
Solution-IDContentsSolvent system
11.3 mM [U-100% 13C; U-100% 15N] SoR190, 5 mM CaCl2, 100 mM sodium chloride, 20 mM ammonium acetate, 10 mM DTT, 0.02 % NaN3, 95% H2O/5% D2O95% H2O/5% D2O
21.3 mM [U-5% 13C; U-100% 15N] SoR190, 5 mM CaCl2, 100 mM sodium chloride, 20 mM ammonium acetate, 10 mM DTT, 0.02 % NaN3, 95% H2O/5% D2O95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1.3 mMSoR190[U-100% 13C; U-100% 15N]1
5 mMCaCl21
100 mMsodium chloride1
20 mMammonium acetate1
10 mMDTT1
0.02 %NaN31
1.3 mMSoR190[U-5% 13C; U-100% 15N]2
5 mMCaCl22
100 mMsodium chloride2
20 mMammonium acetate2
10 mMDTT2
0.02 %NaN32
Sample conditionsIonic strength: 0.1 M / pH: 5.5 / Pressure: ambient / Temperature: 293 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE8001
Bruker AvanceBrukerAVANCE6002

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Processing

NMR software
NameVersionDeveloperClassification
TopSpin2.1Bruker Biospincollection
AutoAssign2.2.1Zimmerman, Moseley, Kulikowski and Montelionechemical shift assignment
Sparky3.11Goddardpeak picking
Sparky3.11Goddarddata analysis
AutoStructure2.2.1Huang, Tejero, Powers and Montelionestructure solution
NMRPipe2.3Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
CYANA2.1Guntert, Mumenthaler and Wuthrichstructure solution
CNS1.1Brunger, Adams, Clore, Gros, Nilges and Readrefinement
PSVS1.3Bhattacharya and Montelionedata analysis
PdbStat5Tejero and Montelionepdbanalysis
RefinementMethod: simulated annealing / Software ordinal: 1
Details: THE STRUCTURES ARE BASED ON A TOTAL OF 2291 COMFORMATIONALLY-RESTRICTING NOE-DERIVED DISTANCE CONSTRAINTS, 146 DIHEDRAL ANGLE CONSTRAINTS, AND 92 HYDROGEN BOND CONSTRAINTS (22.4 CONSTRAINTS ...Details: THE STRUCTURES ARE BASED ON A TOTAL OF 2291 COMFORMATIONALLY-RESTRICTING NOE-DERIVED DISTANCE CONSTRAINTS, 146 DIHEDRAL ANGLE CONSTRAINTS, AND 92 HYDROGEN BOND CONSTRAINTS (22.4 CONSTRAINTS PER RESIDUE, 7.7 LONG RANGE CONSTRAINTS PER RESIDUE, COMPUTED FOR RESIDUES 1 TO 118 BY PSVS 1.3) STRUCTURE DETERMINATION WAS PERFORMED ITERATIVELY USING AUTOSTRUCTURE AND CYANA. 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 (HHHHHH) WERE INCLUDED IN ALL STRUCTURE CALCULATIONS AND HAVE BEEN INCLUDED IN THIS DEPOSITION. COORDINATES FOR THE FOLLOWING RESIDUES ARE NOT WELL DETERMINED (S(PHI)+S(PSI)<1.8): 1-3, 21-22, 112-118. THE STRUCTURE WAS DETERMINED USING TRIPLE RESONANCE NMR SPECTROSCOPY. AUTOMATED BACKBONE ASSIGNMENTS WERE MADE USING AUTOASSIGN AND THE SIDE CHAIN ASSIGNMENTS WERE COMPLETED MANUALLY. AUTOMATIC NOESY ASSIGNMENTS AS WELL AS DISTANCE, DIHEDRAL ANGLE (TALOS) AND HYDROGEN BOND CONSTRAINTS WERE DETERMINED USING CYANA. COMPLETENESS OF NMR ASSIGNMENT: BACKBONE, 94.10%, SIDE CHAIN, 82.27%, AROMATICS, 76.92%, STEREOSPECIFIC METHYL, 91.67%, FINAL STRUCTURE QUALITY FACTORS (FOR RESIDUE 1-118 PSVS 1.3), WHERE ORDERED RESIDUE RANGES (S(PHI)+S(PSI)>1.8) COMPRISE: 4-20, 23-111. (A) RMSD (ORDERED RESIDUES): BB 0.6, HEAVY ATOM: 1.1 (B) RAMACHANDRAN STATISTICS FOR ORDERED RESIDUES: MOST FAVORED, 88.1%, ADDITIONALLY ALLOWED: 11.8%, GENEROUSLY ALLOWED : 0.1%, DISALLOWED, 0.0%. (C) PROCHECK SCORES FOR ORDERED RESIDUES (RAW/Z): PHI-PSI, -0.30/-0.87, ALL , -0.12/-0.71. (D) MOLPROBITY CLASH SCORE (RAW/Z): 13.32/-0.76. (E) RPF SCORES FOR GOODNESS OF FIT TO NOESY DATA (RESIDUE 1-118): RECALL, 1, PRECISION, 0.975, F-MEASURE, 0.987, DP-SCORE, 0.89.
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20 / Maximum upper distance constraint violation: 0.22 Å
NMR ensemble rmsDistance rms dev: 0.01 Å

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