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- PDB-2jro: Solution NMR Structure of SO0334 from Shewanella oneidensis. Nort... -

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Basic information

Entry
Database: PDB / ID: 2jro
TitleSolution NMR Structure of SO0334 from Shewanella oneidensis. Northeast Structural Genomics Target SoR75
ComponentsUncharacterized protein
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / solution NMR structure / PSI-2 / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG
Function / homologyso0334 like domain / Protein of unknown function DUF1107 / Protein of unknown function (DUF1107) / so0334 like fold / 2-Layer Sandwich / Alpha Beta / Uncharacterized protein
Function and homology information
Biological speciesShewanella oneidensis (bacteria)
MethodSOLUTION NMR / simulated annealing
AuthorsTang, Y. / Wang, D. / Nwosu, C. / Cunningham, K. / Xiao, R. / Liu, J. / Baran, M.C. / Swapna, G. / Acton, T.B. / Rost, B. ...Tang, Y. / Wang, D. / Nwosu, C. / Cunningham, K. / Xiao, R. / Liu, J. / Baran, M.C. / Swapna, G. / Acton, T.B. / Rost, B. / Montelione, G.T. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published
Title: Solution Structure of SO0334 from Shewanella oneidensis.
Authors: Tang, Y. / Wang, D. / Nwosu, C. / Cunningham, K. / Xiao, R. / Liu, J. / Baran, M.C. / Swapna, G. / Acton, T.B. / Rost, B. / Montelione, G.T.
History
DepositionJun 28, 2007Deposition site: BMRB / Processing site: RCSB
Revision 1.0Aug 21, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.2May 1, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer / 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_software.name / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)9,2251
Polymers9,2251
Non-polymers00
Water0
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 Uncharacterized protein


Mass: 9224.935 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Shewanella oneidensis (bacteria) / Strain: MR-1
Description: The protein is a monomer by gel filtration chromatography and static light scattering.
Gene: SO_0334 / Plasmid details: pET21 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)+Magic / References: UniProt: Q8EJX2

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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 1H-13C NOESY
1513D 1H-13C NOESY aromatic
1613D HNCO
1713D HN(CA)CB
1813D NH(CO)CACB
1913D HBHA(CO)NH
11013D (H)CCH-TOCSY
11113D (H)CCH-COSY
11213D CCH-TOCSY
11322D 1H-13C HSQC high resolution

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Sample preparation

Details
Solution-IDContentsSolvent system
11.1 mM [U-100% 13C; U-100% 15N] protein, 20 mM MES, 100 mM NaCl, 5 mM CaCl2, 10 mM DTT, 0.02 % NaN3, 95% H2O/5% D2O95% H2O/5% D2O
20.95 mM [U-5% 13C; U-100% 15N] protein, 20 mM MES, 100 mM NaCl, 5 mM CaCl2, 10 mM DTT, 0.02 % NaN3, 95% H2O/5% D2O95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1.1 mMSoR75[U-100% 13C; U-100% 15N]1
20 mMMES1
100 mMNaCl1
5 mMCaCl21
10 mMDTT1
0.02 %NaN31
0.95 mMSoR75[U-5% 13C; U-100% 15N]2
20 mMMES2
100 mMNaCl2
5 mMCaCl22
10 mMDTT2
0.02 %NaN32
Sample conditionsIonic strength: 100 / pH: 6.5 / 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
TopSpin1.3Bruker Biospincollection
AutoAssign2.2.1Zimmerman, Moseley, Kulikowski and Montelionechemical shift assignment
Sparky3.11Goddardpeak picking
Sparky3.11Goddarddata analysis
AutoStructure2.1.1Huang, Tejero, Powers and Montelionestructure solution
NMRPipe2.3Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
X-PLOR NIH2.11.2Schwieters, Kuszewski, Tjandra and Clorestructure solution
X-PLOR NIH2.11.2Schwieters, Kuszewski, Tjandra and Clorerefinement
CNS1.1Brunger, Adams, Clore, Gros, Nilges and Readstructure solution
CNS1.1Brunger, Adams, Clore, Gros, Nilges and Readrefinement
PSVS1.3Bhattacharya and Montelionedata analysis
PdbStat4Tejero and Montelionepdb analysis
CYANAGuntert, Mumenthaler and Wuthrichstructure solution
RefinementMethod: simulated annealing / Software ordinal: 1
Details: THE STRUCTURES ARE BASED ON A TOTAL OF 1006 CONFORMATIONALLY-RESTRICTING NOE-DERIVED DISTANCE CONSTRAINTS, 68 DIHEDRAL ANGLE CONSTRAINTS, AND 42 HYDROGEN BOND CONSTRAINTS (15.3 CONSTRAINTS ...Details: THE STRUCTURES ARE BASED ON A TOTAL OF 1006 CONFORMATIONALLY-RESTRICTING NOE-DERIVED DISTANCE CONSTRAINTS, 68 DIHEDRAL ANGLE CONSTRAINTS, AND 42 HYDROGEN BOND CONSTRAINTS (15.3 CONSTRAINTS PER RESIDUE, 4.2 LONG RANGE CONSTRAINTS PER RESIDUE, COMPUTED FOR RESIDUES 1 TO 74 BY PSVS 1.3) 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 RESDIUES OF THE PROTEIN (HHHH) WERE INCLUDED IN ALL STRUCTURE CALCULATIONS BUT HAVE BEEN OMITTED FROM THIS DEPOSITION. COORDINATES FOR THE FOLLOWING RESIDUES ARE NOT WELL DETERMINED(S(PHI)+S(PSI)<1.8): 1, 6-8, 39-46, 65-74. THE STRUCTURE WAS DETERMINED USING TRIPLE RESONANCE NMR SPECTROSCOPY. AUTOMATED BACKBONE ASSIGNMENTS WERE MADE USING AUTOASSIGN AND THE SIDE CHAIN ASSIGNMENT WERE COMPLETED MANUALLY. AUTOMATIC NOESY ASSIGNMENTS AS WELL AS DISTANCE, DIHEDRAL ANGLE (HYPER) AND HYDROGEN BOND CONSTRAINTS WERE DETERMINED USING AUTOSTRUCTURE. COMPLETENESS OF NMR ASSIGNMENT (EXCLUDING C-TERMINAL HHHH): BACKBONE,98.87%, SIDE CHAIN, 94.56%, AROMATICS, 100%, STEREOSPECIFIC METHYL, 88.23%, FINAL STRUCTURE QUALITY FACTORS (FOR RESIDUE 1-74 PSVS 1.3), WHERE ORDERED RESIDUES (S(PHI)+S(PSI)>1.8) COMPRISE: 2-5, 9-38, 47-64.. (A) RMSD (ORDERED RESIDUES): BB 0.6, HEAVY ATOM: 1.1 (B) RAMACHANDRAN STATISTICS FOR ORDERED RESIDUES: MOST FAVORED, 91.85%, ADDITIONALLY ALLOWED: 8.5%, GENEROUSLY ALLOWED : 0.0%, DISALLOWED, 0.0%. (C) PROCHECK SCORES FOR ORDERED RESIDUES (RAW/Z): PHI-PSI, -0.11/-0.12, ALL , -0.14/-0.83. (D) MOLPROBITY CLASH SCORE (RAW/Z): 19.48/-1.82. (E) RPF SCORES FOR GOODNESS OF FIT TO NOESY DATA (RESIDUE 1-60): RECALL, 0987, PRECISION, 0.914, F-MEASURE, 0.949, DP-SCORE, 0.788.
NMR constraintsNOE constraints total: 1006 / NOE intraresidue total count: 191 / NOE long range total count: 297 / NOE medium range total count: 210 / NOE sequential total count: 308
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 torsion angle constraint violation: 7.3 ° / Maximum upper distance constraint violation: 0.4 Å
NMR ensemble rmsDistance rms dev: 0.02 Å

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