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- PDB-2lse: Solution NMR Structure of De Novo Designed Four Helix Bundle Prot... -

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Basic information

Entry
Database: PDB / ID: 2lse
TitleSolution NMR Structure of De Novo Designed Four Helix Bundle Protein, Northeast Structural Genomics Consortium (NESG) Target OR188
ComponentsFour Helix Bundle Protein
KeywordsDE NOVO PROTEIN / Structural Genomics / NORTHEAST STRUCTURAL GENOMICS CONSORTIUM / NESG / PSI-Biology / Protein Structure Initiative
Function / homologyFour Helix Bundle (Hemerythrin (Met), subunit A) - #1360 / Four Helix Bundle (Hemerythrin (Met), subunit A) / Up-down Bundle / Mainly Alpha
Function and homology information
Biological speciesartificial gene (others)
MethodSOLUTION NMR / simulated annealing, molecular dynamics
Model detailslowest energy, model 1
AuthorsSathyamoorthy, B. / Pulavarti, S. / Murphy, G. / Mills, J.L. / Eletski, A. / Der, B.S. / Machius, M.C. / Kuhlman, B. / Montelione, G.T. / Szyperski, T. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published
Title: Solution NMR Structure of a Denovo Design Four Helix Bundle Protein, Northeast Structural Genomics Consortium Target OR188
Authors: Murphy, G. / Sathyamoorthy, B. / Der, B.S. / Machius, M.C. / Pulavarti, S. / Montelione, G.T. / Szyperski, T. / Kuhlman, B.
History
DepositionApr 28, 2012Deposition site: BMRB / Processing site: RCSB
Revision 1.0Jun 27, 2012Provider: repository / Type: Initial release
Revision 1.1Jun 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 1.2May 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: Four Helix Bundle Protein


Theoretical massNumber of molelcules
Total (without water)11,9281
Polymers11,9281
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 Four Helix Bundle Protein


Mass: 11927.562 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) artificial gene (others) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pMgK

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1213D HN(CA)CO
1313D HNCO
141(4,3)D GFT CABCA(CO)NH
151(4,3)D GFT HNCACAB
161(4,3)D GFT HABCAB(CO)NH
1713D simutaneous 13C-aromatic,13C-aliphatic,15N edited 1H-1H NOESY
1812D 1H-13C HSQC aliphatic CT
1912D 1H-13C HSQC aromatic CT
1101(4,3)D GFT (H)CCH-COSY aliphatic SP1/SP2/CP
11113D (H)CCH-TOCSY
11213D C(CO)NH
11313D H(CCO)NH
1141(4,3)D GFT (H)CCH-COSY aromatic SP1/SP2/CP
11522D 1H-13C HSQC aliphatic 28ms CT
11622D 1H-13C HSQC aliphatic 42ms CT
11722D 1H-13C HSQC aliphatic 56ms CT

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Sample preparation

Details
Solution-IDContentsSolvent system
123.8 mg/mL [U-100% 13C; U-100% 15N] OR188.001, 100 mM phosphate, 100 mM NaCl, 90% H2O/10% D2O90% H2O/10% D2O
21.3 mg/mL [U-10% 13C; U-100% 15N] OR188.001, 100 mM phosphate, 100 mM NaCl, 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
23.8 mg/mLOR188.001-1[U-100% 13C; U-100% 15N]1
100 mMphosphate-21
100 mMNaCl-31
1.3 mg/mLOR188.001-4[U-10% 13C; U-100% 15N]2
100 mMphosphate-52
100 mMNaCl-62
Sample conditionspH: 7 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA7501
Varian INOVAVarianINOVA6002

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Processing

NMR software
NameVersionDeveloperClassification
CNSBrunger, Adams, Clore, Gros, Nilges and Readrefinement
CNSBrunger, Adams, Clore, Gros, Nilges and Readstructure solution
CNSBrunger, Adams, Clore, Gros, Nilges and Readgeometry optimization
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
PROSAGuntertprocessing
XEASYBartels et al.processing
XEASYBartels et al.data analysis
VnmrJ2.2DVariancollection
TALOS+Shen, Cornilescu, Delaglio and Baxgeometry optimization
PSVSBhattacharya, Montelionestructure validation
CARA1,8Keller and Wuthrichchemical shift assignment
CARA1,8Keller and Wuthrichdata analysis
CARA1,8Keller and Wuthrichchemical shift calculation
CARA1,8Keller and Wuthrichpeak picking
CARA1,8Keller and Wuthrichrefinement
CSI2David Wishart, Brian Sykesdata analysis
MOLMOL2K.2Koradi, Billeter and Wuthrichstructure solution
MOLMOL2K.2Koradi, Billeter and Wuthrichvisualization
RefinementMethod: simulated annealing, molecular dynamics / Software ordinal: 1 / Details: Cyana3, Waterbath
NMR constraintsNOE constraints total: 1621 / NOE intraresidue total count: 335 / NOE long range total count: 447 / NOE medium range total count: 464 / NOE sequential total count: 375 / Protein phi angle constraints total count: 63 / Protein psi angle constraints total count: 63
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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