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- PDB-2lch: Solution NMR Structure of a Protein With a Redesigned Hydrophobic... -

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Basic information

Entry
Database: PDB / ID: 2lch
TitleSolution NMR Structure of a Protein With a Redesigned Hydrophobic Core, Northeast Structural Genomics Consortium Target OR38
ComponentsProtein OR38
KeywordsDE NOVO PROTEIN / Structural Genomics / NORTHEAST STRUCTURAL GENOMICS CONSORTIUM / NESG / PSI-Biology / Protein Structure Initiative
Function / homologyHPT domain / Four Helix Bundle (Hemerythrin (Met), subunit A) / Up-down Bundle / Mainly Alpha
Function and homology information
Biological speciesThermotoga maritima (bacteria)
MethodSOLUTION NMR / simulated annealing, torsion angle dynamics, molecular dynamics
Model detailslowest energy, model 1
AuthorsMills, J.L. / Murphy, G. / Miley, M. / Machius, M. / Kuhlman, B. / Montelione, G.T. / Szyperski, T. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published
Title: Solution NMR Structure of a Protein With a Redesigned Hydrophobic Core, Northeast Structural Genomics Consortium Target OR38
Authors: Mills, J.L. / Murphy, G. / Miley, M. / Machius, M. / Kuhlman, B. / Montelione, G.T. / Szyperski, T.
History
DepositionApr 29, 2011Deposition site: BMRB / Processing site: RCSB
Revision 1.0May 25, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 22, 2012Group: Structure summary
Revision 1.3Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status / pdbx_nmr_software
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data / _pdbx_nmr_software.name
Revision 1.4May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Protein OR38


Theoretical massNumber of molelcules
Total (without water)13,2661
Polymers13,2661
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 Protein OR38


Mass: 13266.452 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (bacteria) / Production host: Escherichia coli (E. coli)

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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 HNCO
1413D CBCA(CO)NH
1513D HN(CA)CB
1613D simutaneous 13C-aromatic,13C-aliphatic,15N edited 1H-1H NOESY
1713D HBHA(CO)NH
1813D (H)CCH-TOCSY
1913D (H)CCH-COSY
11022D 1H-15N HSQC
11113D HN(CA)CO

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Sample preparation

Details
Solution-IDContentsSolvent system
11.0 mM [U-100% 13C; U-100% 15N] OR38, 100 mM sodium phosphate, 50 mM sodium chloride, 95% H2O/5% D2O95% H2O/5% D2O
21.0 mM [U-10% 13C; U-100% 15N] OR38, 100 mM sodium phosphate, 50 mM sodium chloride, 95% H2O/5% D2O95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1.0 mMOR38-1[U-100% 13C; U-100% 15N]1
100 mMsodium phosphate-21
50 mMsodium chloride-31
1.0 mMOR38-4[U-10% 13C; U-100% 15N]2
100 mMsodium phosphate-52
50 mMsodium chloride-62
Sample conditionspH: 6.5 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 750 MHz

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Processing

NMR software
NameVersionDeveloperClassification
CARA1.8Keller et al.data analysis
CARA1.8Keller et al.peak picking
CARA1.8Keller et al.chemical shift assignment
CYANA3Guntert, Mumenthaler and Wuthrichrefinement
CYANA3Guntert, Mumenthaler and Wuthrichgeometry optimization
CYANA3Guntert, Mumenthaler and Wuthrichstructure solution
AutoStructure2.1Huang, Tejero, Powers and Montelionedata analysis
AutoStructure2.1Huang, Tejero, Powers and Montelionerefinement
AutoAssign2.1Zimmerman, Moseley, Kulikowski and Montelionedata analysis
AutoAssign2.1Zimmerman, Moseley, Kulikowski and Montelionechemical shift assignment
VnmrJVariancollection
PINEBahrami, Markley, Assadi, and Eghbalniachemical shift assignment
TALOS+Shen, Cornilescu, Delaglio and Baxgeometry optimization
CNSBrunger, Adams, Clore, Gros, Nilges and Readrefinement
RefinementMethod: simulated annealing, torsion angle dynamics, molecular dynamics
Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20

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