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- PDB-2k5r: Solution NMR Structure of XF2673 from Xylella fastidiosa. Northea... -

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Basic information

Entry
Database: PDB / ID: 2k5r
TitleSolution NMR Structure of XF2673 from Xylella fastidiosa. Northeast Structural Genomics Consortium Target XfR39
Componentsuncharacterized protein XF2673
Keywordsstructural genomics / unknown function / solution NMR structure / PSI-2 / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG
Function / homologyTrm112-like / Trm112p-like protein / Uncharacterized protein
Function and homology information
Biological speciesXylella fastidiosa Temecula1 (bacteria)
MethodSOLUTION NMR / simulated annealing
AuthorsTang, Y. / Wang, H. / Jiang, M. / Maglaqui, M. / Xiao, R. / Liu, J. / Baran, M.C. / Swapna, G. / Acton, T.B. / Rost, B. ...Tang, Y. / Wang, H. / Jiang, M. / Maglaqui, M. / 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 NMR Structure of XF2673 from Xylella fastidiosa. Northeast Structural Genomics Consortium Target XfR39
Authors: Tang, Y. / Wang, H. / Jiang, M. / Maglaqui, M. / Xiao, R. / Liu, J. / Baran, M.C. / Swapna, G. / Acton, T.B. / Rost, B. / Montelione, G.T.
History
DepositionJun 30, 2008Deposition site: BMRB / Processing site: RCSB
Revision 1.0Aug 26, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 19, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: pdbx_database_status / pdbx_nmr_software ...pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: uncharacterized protein XF2673


Theoretical massNumber of molelcules
Total (without water)11,0011
Polymers11,0011
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 XF2673


Mass: 11000.567 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: residue 90-97 represent a non-native purification tag (LEHHHHHH)
Source: (gene. exp.) Xylella fastidiosa Temecula1 (bacteria)
Species: fastidiosa
Description: C-terminal tag LEHHHHHH. The protein is a monomer by gel filtration chromatography and static light scattering
Gene: PD_2037 / Plasmid: XfR39-21.3 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)+magic / References: UniProt: Q87A02

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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
1312D 1H-13C HSQC armatic
1413D CBCA(CO)NH
1513D HBHA(CO)NH
1613D HN(CA)CB
1713D (H)CCH-TOCSY
1813D (H)CCH-COSY
1913D CCH-TOCSY
11013D HNCO
11113D 1H-15N NOESY
11213D simutaeous NOESY
11313D 1H-13C NOESY aromatic
11422D 1H-13C HSQC high resolution

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Sample preparation

Details
Solution-IDContentsSolvent system
11.0 mM [U-100% 13C; U-100% 15N] XfR39, 20 mM MES, 100 mM NaCl, 5 mM CaCl2, 10 mM DTT, 0.02 % NaN3, 50 uM DSS, 95% H2O/5% D2O95% H2O/5% D2O
21.0 mM [U-5% 13C; U-100% 15N] XfR39, 20 mM MES, 100 mM NaCl, 5 mM CaCl2, 10 mM DTT, 0.02 % NaN3, 50 uM DSS, 95% H2O/5% D2O95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1.0 mMXfR39[U-100% 13C; U-100% 15N]1
20 mMMES1
100 mMNaCl1
5 mMCaCl21
10 mMDTT1
0.02 %NaN31
50 uMDSS1
1.0 mMXfR39[U-5% 13C; U-100% 15N]2
20 mMMES2
100 mMNaCl2
5 mMCaCl22
10 mMDTT2
0.02 %NaN32
50 uMDSS2
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
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
CYANA2.1Guntert, Mumenthaler and Wuthrichstructure solution
NMRPipe2.3Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
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 1591 COMFORMATIONALLY-RESTRICTING NOE-DERIVED DISTANCE CONSTRAINTS, 100 DIHEDRAL ANGLE CONSTRAINTS, AND 42 HYDROGEN BOND CONSTRAINTS (18.8 CONSTRAINTS ...Details: THE STRUCTURES ARE BASED ON A TOTAL OF 1591 COMFORMATIONALLY-RESTRICTING NOE-DERIVED DISTANCE CONSTRAINTS, 100 DIHEDRAL ANGLE CONSTRAINTS, AND 42 HYDROGEN BOND CONSTRAINTS (18.8 CONSTRAINTS PER RESIDUE, 4.4 LONG RANGE CONSTRAINTS PER RESIDUE, COMPUTED FOR RESIDUES 1 TO 97 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: 1-17, 67-68, 88-97. 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, 91.81%, SIDE CHAIN, 80.87%, AROMATICS, 60.00%, STEREOSPECIFIC METHYL, 82.35%, FINAL STRUCTURE QUALITY FACTORS (FOR RESIDUE 1-97 PSVS 1.3), WHERE ORDERED RESIDUE RANGES COMPRISE: 18-66, 69-87. (A) RMSD (ORDERED RESIDUES): BB 0.82, HEAVY ATOM: 1.46 (B) RAMACHANDRAN STATISTICS FOR ORDERED RESIDUES: MOST FAVORED, 92.8%, ADDITIONALLY ALLOWED: 7.2%, GENEROUSLY ALLOWED : 0.0%, DISALLOWED, 0.0%. (C) PROCHECK SCORES FOR ORDERED RESIDUES (RAW/Z): PHI-PSI, -0.30/-0.87, ALL , -0.26/-1.54. (D) MOLPROBITY CLASH SCORE (RAW/Z): 16.58/-1.32. (E) RPF SCORES FOR GOODNESS OF FIT TO NOESY DATA (RESIDUE 1-97): RECALL, 1, PRECISION, 0.979, F-MEASURE, 0.99, DP-SCORE, 0.823.
NMR constraintsProtein chi angle constraints total count: 0 / Protein other angle constraints total count: 0 / Protein phi angle constraints total count: 50 / Protein psi angle constraints total count: 50
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: 4.6 ° / Maximum upper distance constraint violation: 0.25 Å
NMR ensemble rmsDistance rms dev: 0.01 Å

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