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- PDB-2do8: Solution Structure of UPF0301 protein HD_1794 -

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Basic information

Entry
Database: PDB / ID: 2do8
TitleSolution Structure of UPF0301 protein HD_1794
ComponentsUPF0301 protein HD_1794
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / NESG / GFT NMR / STRUCTRAL GENOMICS / HdR14 / PSI / Protein Structure Initiative / Northeast Structural Genomics Consortium
Function / homologyVC0467-like / VC0467-like / Protein of unknown function UPF0301 / Uncharacterized ACR, COG1678 / 3-Layer(aba) Sandwich / Alpha Beta / UPF0301 protein HD_1794
Function and homology information
Biological speciesHaemophilus ducreyi (bacteria)
MethodSOLUTION NMR / distance geometry, simulated annealing, molecular dynamics, torsion angle dynamics
AuthorsZhang, Q. / Liu, G. / Shastry, R. / Jiang, M. / Cunningham, K. / Ma, L.C. / Xiao, R. / Acton, T.R. / Montelione, G.T. / Szyperski, T. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be published
Title: Solution Structure of UPF0301 protein HD_1794
Authors: Zhang, Q. / Liu, G. / Shastry, R. / Jiang, M. / Cunningham, K. / Ma, L.C. / Xiao, R. / Acton, T.R. / Montelione, G.T. / Szyperski, T.
History
DepositionApr 27, 2006Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 25, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 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: UPF0301 protein HD_1794


Theoretical massNumber of molelcules
Total (without water)21,2621
Polymers21,2621
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 least restraint violations
RepresentativeModel #1lowest energy

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Components

#1: Protein UPF0301 protein HD_1794


Mass: 21261.820 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Haemophilus ducreyi (bacteria) / Gene: OrderedLocusNames: HD_1794 / Production host: Escherichia coli (E. coli) / References: UniProt: Q7VKS7

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111GFT (4,3)D HNNCABCA
121GFT (4,3)D CABCA(CO)NHN
131GFT (4,3)D HABCAB(CO)NHN
141GFT (4,3)D (H)CCH
151SIMULTANEOUS HETERONUCLEAR RESOLVED [1H,1H]-NOESY
NMR detailsText: This structure was determined using GFT techniques.

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Sample preparation

DetailsContents: 50mM MES; 10mM DTT; 50mM Arginine; 0.02% NaN3; 95% H2O, 5% D2O
Solvent system: 95% H2O/5% D2O
Sample conditionspH: 6 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA6001
Varian INOVAVarianINOVA7502

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Processing

NMR software
NameVersionDeveloperClassification
DYANA1.5Guntert, P.structure solution
CYANA2.1Guntert, P.structure solution
NMRPipe2.3Delaglio, F.processing
CNS1.1refinement
XEASY1.3Bartels, C., Xia, T.data analysis
UBNMR1Shen, Y.data analysis
AutoStructure2.0.0Huang, Y.J.data analysis
RefinementMethod: distance geometry, simulated annealing, molecular dynamics, torsion angle dynamics
Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 100 / Conformers submitted total number: 20

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