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- PDB-2k53: NMR solution structure of A3DK08 protein from Clostridium thermoc... -

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Basic information

Entry
Database: PDB / ID: 2k53
TitleNMR solution structure of A3DK08 protein from Clostridium thermocellum: Northeast Structural Genomics Consortium Target CmR9
ComponentsA3DK08 Protein
Keywordsstructural genomics / unknown function / NESG / CmR9 / Clostridium thermocellum / A3DK08 protein / PSI-2 / Protein Structure Initiative / Northeast Structural Genomics Consortium
Function / homologyConserved hypothetical protein CHP03980, redox-disulphide / SP0561-like / SP0561-like / Domain of unknown function DUF1858 / ScdA-like, N-terminal domain superfamily / Domain of unknown function (DUF1858) / Orthogonal Bundle / Mainly Alpha / DUF1858 domain-containing protein
Function and homology information
Biological speciesClostridium thermocellum ATCC 27405 (bacteria)
MethodSOLUTION NMR / simulated annealing
AuthorsSwapna, G.V.T. / Huang, W. / Jiang, M. / Foote, E.L. / Xiao, R. / Nair, R. / Everett, J. / Acton, T.B. / Rost, B. / Montelione, G.T. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published
Title: NMR Solution Structure of A3DK08 protein from Clostridium thermocellum: Northeast Structural Genomics Consortium Target CmR9
Authors: Swapna, G.V.T. / Huang, W. / Jiang, M. / Foote, E.L. / Xiao, R. / Nair, R. / Everett, J. / Acton, T.B. / Rost, B. / Montelione, G.T.
History
DepositionJun 24, 2008Deposition site: BMRB / Processing site: RCSB
Revision 1.0Aug 19, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 16, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list
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
Revision 1.3May 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: A3DK08 Protein


Theoretical massNumber of molelcules
Total (without water)8,5961
Polymers8,5961
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 A3DK08 Protein


Mass: 8595.886 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridium thermocellum ATCC 27405 (bacteria)
Species: thermocellum / Gene: Cthe_3092 / Plasmid: pET 21-23C / Species (production host): coli / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)+magic / References: UniProt: A3DK08

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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-15N HSQC
1312D 1H-13C HSQC
2422D 1H-13C HSQC
1513D CBCA(CO)NH
1613D HN(CA)CB
1713D HNCO
1813D HBHA(CO)NH
1913D (H)CCH-TOCSY
11013D 1H-13C NOESY
11113D 1H-15N NOESY
11213D 1H-13C NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
10.91 mM [U-100% 13C; U-100% 15N] A3DK08 Protein, 90% H2O/10% D2O90% H2O/10% D2O
21.05 mM [U-10% 13C; U-99% 15N] A3DK08 Protein, 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.91 mMA3DK08 Protein[U-100% 13C; U-100% 15N]1
1.05 mMA3DK08 Protein[U-10% 13C; U-99% 15N]2
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
15mM CaCl2, 100mM NaCl 6.51 atm293 K
25mM CaCl2, 100mM NaCl 6.51 atm293 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA6001
Bruker AvanceBrukerAVANCE8002

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Processing

NMR software
NameVersionDeveloperClassification
CNS2.0.6Brunger, Adams, Clore, Gros, Nilges and Readrefinement
CYANA2.1Guntert, Mumenthaler and Wuthrichstructure solution
AutoAssign2.4.0Zimmerman, Moseley, Kulikowski and Montelionechemical shift assignment
AutoStructure2.2.1Huang, Tejero, Powers and Montelionenoesy assignments
RefinementMethod: simulated annealing / Software ordinal: 1
Details: The structure was determined using triple resonance NMR spectroscopy. Automated backbone resonance assignments were made using AUTOASSIGN and the sidechain assignments were completed ...Details: The structure was determined using triple resonance NMR spectroscopy. Automated backbone resonance assignments were made using AUTOASSIGN and the sidechain assignments were completed manually. Automated NOESY assignments were made using AUTOSTRUCTURE and CYANA-2.1. Dihedral angle constraints were obtained from TALOS. The structure calculations were done excluding the six HIS from the 8-residue C-terminal tag(LEHHHHHH). Completeness of assignments excluding the HHHHHH: Backbone:100% Sidechain(aliphatic): 99% Sidechain (Aromatic): 90% Stereospecific Methyl assignments:100%. The assignments were validated using AVS software. Final structure quality factors(excluding the HHHHHH) determined using PSVS-v1.3: Ordered residues are defined as residues 2-28,33-34,37-69.(a) RMSD (ordered residues)all backbone atoms:0.4A, all heavy atoms: 0.7A; RMSD (all residues) backbone: 0.7A and heavy atoms: 1.0A. (b) Ramachandran statistics for ordered residues : Most favoured regions: 97.1%, additionally allowed regions: 2.9%.(C) PROCHECK SCORES FOR ORDERED RESIDUES (RAW/Z-): PHI-PSI,0.21/1.14, ALL,0.24/1.42 (D) MOLPROBITY CLASH SCORE (RAW/Z-): 17.26/-1.44. (E) RPF scores for the goodness of the fit to NOESY data: Recall:0.984, PRECISION: 0.848, F-measure: 0.911 and final DP-score:0.743. (f) Number of close contacts for 20 models: 6. RMS deviation for bond angles:0.6deg. RMS deviation for bond lengths 0.008A.
NMR constraintsNOE constraints total: 854 / NOE intraresidue total count: 325 / NOE long range total count: 160 / NOE medium range total count: 134 / NOE sequential total count: 185 / Protein phi angle constraints total count: 45 / Protein psi angle constraints total count: 45
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: 0.2 Å / Torsion angle constraint violation method: PSVS software
NMR ensemble rmsDistance rms dev: 0.01 Å

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