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- PDB-2gm2: NMR structure of Xanthomonas campestris XCC1710: Northeast Struct... -

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Basic information

Entry
Database: PDB / ID: 2gm2
TitleNMR structure of Xanthomonas campestris XCC1710: Northeast Structural Genomics Consortium target XcR35
Componentsconserved hypothetical protein
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / MTH938-like fold / PSI / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG
Function / homologyHypothetical Protein Mth938; Chain: A, / MTH938-like / NDUFAF3/Mth938 domain-containing protein / MTH938-like superfamily / Protein of unknown function (DUF498/DUF598) / 3-Layer(aba) Sandwich / Alpha Beta / : / Xcc1710-like domain-containing protein
Function and homology information
Biological speciesXanthomonas campestris pv. campestris str. ATCC 33913 (bacteria)
MethodSOLUTION NMR / THE INITIAL STRUCTURE WAS DETERMINED USING AUTOMATED STRUCTURE DETERMINATION (AUTOSTRUCTURE), REFINED MANUALLY. A FINAL REFINEMENT USED SIMULTATED ANNEALING IN EXPLICIT SOLVENT.
AuthorsCort, J.R. / Xiao, R. / Wang, D.Y. / Ma, L.C. / Ciano, M. / Montelione, G.T. / Ramelot, T.A. / Kennedy, M.A. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published
Title: NMR structure of Xanthomonas campestris XCC1710 protein
Authors: Cort, J.R. / Ramelot, T.A. / Montelione, G.T. / Kennedy, M.A.
History
DepositionApr 5, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 25, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 9, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / 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_software.name / _struct_ref_seq_dif.details
Revision 1.4May 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: conserved hypothetical protein


Theoretical massNumber of molelcules
Total (without water)14,4681
Polymers14,4681
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 / 40structures with fewest restraint violations, low restraint violation energies, and acceptable geometry
RepresentativeModel #1closest to the average

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Components

#1: Protein conserved hypothetical protein


Mass: 14468.479 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xanthomonas campestris pv. campestris str. ATCC 33913 (bacteria)
Species: Xanthomonas campestris / Strain: pv. campestris str. ATCC 33913 / Gene: XCC1710 / Plasmid: pET21 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)+Magic / References: GenBank: 21112802, UniProt: Q8P9Y3*PLUS

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 15N-separated NOESY
1213D 13C-separated NOESY
1323D 13C-separated NOESY
1424D 13C-separated NOESY
151HNHA

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Sample preparation

Details
Solution-IDContentsSolvent system
10.5 mM XCC1710pH 6.5 MES, 100 mM NaCl, 20 mM CaCl2, 10 mM DTT, 0.02% NaN3, 5% D2O
20.5 mM XCC1710pH 6.5 MES, 100 mM NaCl, 20 mM CaCl2, 10 mM DTT, 0.02% NaN3, 100% D2O
Sample conditionsIonic strength: 100 mM NaCl, 20 mM CaCl2 / pH: 6.5 / Pressure: ambient / Temperature: 298 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian UNITYPLUSVarianUNITYPLUS5001
Varian INOVAVarianINOVA6002
Varian INOVAVarianINOVA7503

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Processing

NMR software
NameVersionDeveloperClassification
VNMR6.1.CVariancollection
Felix98MSIprocessing
Sparky3.106T.D. Goddard & D.G. Knellerdata analysis
AutoStructure2.1.1G.T. Montelione & J. Huangstructure solution
X-PLORNIHA. Brunger et alstructure solution
CNS1.1A. Brunger et alstructure solution
CNS1.1A. Brunger et alrefinement
RefinementMethod: THE INITIAL STRUCTURE WAS DETERMINED USING AUTOMATED STRUCTURE DETERMINATION (AUTOSTRUCTURE), REFINED MANUALLY. A FINAL REFINEMENT USED SIMULTATED ANNEALING IN EXPLICIT SOLVENT.
Software ordinal: 1
Details: THE STRUCTURES ARE BASED ON A TOTAL OF 935 RESTRAINTS. SUMMARY OF EXPERIMENTAL CONSTRAINTS RESTRAINING DISTANCE RESTRAINTS: TOTAL = 758; INTRA-RESIDUE [I=J] = 174; SEQUENTIAL [(I-J)=1] = 174; ...Details: THE STRUCTURES ARE BASED ON A TOTAL OF 935 RESTRAINTS. SUMMARY OF EXPERIMENTAL CONSTRAINTS RESTRAINING DISTANCE RESTRAINTS: TOTAL = 758; INTRA-RESIDUE [I=J] = 174; SEQUENTIAL [(I-J)=1] = 174; MEDIUM RANGE [1<(I-J)<5] = 109; LONG RANGE [(I-J)>=5] = 301; HYDROGEN BOND RESTRAINTS = 56 (2 PER H-BOND); NUMBER OF RESTRAINING DISTANCE RESTRAINTS PER RESTRAINED RESIDUE = 7.3; DIHEDRAL-ANGLE RESTRAINTS = 121 (60 PHI, 59 PSI, 2 CHI-1); TOTAL NUMBER OF RESTRAINTS PER RESTRAINED RESIDUE = 8.3; NUMBER OF LONG RANGE NOE DISTANCE RESTRAINTS PER RESTRAINED RESIDUE = 2.7; NUMBER OF STRUCTURES COMPUTED = 40; NUMBER OF STRUCTURES USED = 20; AVERAGE DISTANCE VIOLATIONS >0.0001 ANG = 19.8 +/- 3.5; AVERAGE R.M.S. DISTANCE VIOLATION = 0.0009 +/- 0.0003 ANG; MAXIMUM NUMBER OF DISTANCE VIOLATIONS 25; MAXIMUM DISTANCE VIOLATION = 0.03 ANG; AVERAGE DIHEDRAL ANGLE VIOLATIONS: >0.0001 DEG = 2.5+/-1.3; MAX NUMBER OF DIHEDRAL ANGLE VIOLATIONS = 4; AVERAGE R.M.S. DIHEDRAL ANGLE VIOLATION = 0.02 +/- .01 DEG.; RMSD VALUES TO AVERAGE STRUCTURE: BACKBONE ATOMS (N,C,C' RESIDUES 12-125) = 0.88 ANG, ALL HEAVY ATOMS = 1.38 ANG; BACKBONE ATOMS (N,C,C' RESIDUES 32-122) = 0.71 ANG, ALL HEAVY ATOMS = 1.21 ANG; BACKBONE ATOMS (N,C,C' RESIDUES 16-17,21-36,39-41,44-46,53-73,76-122) = 0.70 ANG, ALL HEAVY ATOMS = 1.14 ANG; PROCHECK (RESIDUES 16-17,21-36,39-41,44-46,53-73,76-122): MOST FAVORED REGIONS = 84.6%; ADDITIONAL ALLOWED REGIONS = 14.0%; GENEROUSLY ALLOWED REGIONS = 0.2%; DISALLOWED REGIONS = 1.2%; PROCHECK (RESIDUES 12-125): MOST FAVORED REGIONS = 77.8%; ADDITIONAL ALLOWED REGIONS = 19.2%; GENEROUSLY ALLOWED REGIONS = 2.0%; DISALLOWED REGIONS = 1.0%.
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with fewest restraint violations, low restraint violation energies, and acceptable geometry
Conformers calculated total number: 40 / Conformers submitted total number: 20

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