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- PDB-2n8w: Solution NMR Structure of Designed Protein DA05R1, Northeast Stru... -

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Basic information

Entry
Database: PDB / ID: 2n8w
TitleSolution NMR Structure of Designed Protein DA05R1, Northeast Structural Genomics Consortium (NESG) Target OR690
ComponentsDesigned Protein DA05R1
KeywordsDE NOVO PROTEIN / designed protein / PSI-Biology / Structural Genomics / Northeast Structural Genomics Consortium / NESG
Biological speciessynthetic construct (others)
MethodSOLUTION NMR / simulated annealing
Model detailslowest energy, model1
AuthorsEletsky, A. / Federizon, J.F. / Xu, X. / Pulavarti, S. / Jacobs, T.M. / Kuhlman, B. / Szyperski, T. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: Science / Year: 2016
Title: Design of structurally distinct proteins using strategies inspired by evolution.
Authors: Jacobs, T.M. / Williams, B. / Williams, T. / Xu, X. / Eletsky, A. / Federizon, J.F. / Szyperski, T. / Kuhlman, B.
History
DepositionOct 27, 2015Deposition site: BMRB / Processing site: RCSB
Revision 1.0Nov 25, 2015Provider: repository / Type: Initial release
Revision 1.1May 18, 2016Group: Database references
Revision 1.2Jun 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 1.3May 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: Designed Protein DA05R1


Theoretical massNumber of molelcules
Total (without water)11,9321
Polymers11,9321
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 / 100target function
RepresentativeModel #1lowest energy

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Components

#1: Protein Designed Protein DA05R1


Mass: 11932.476 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / 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
1122D 1H-15N HSQC
1222D CT 1H-13C HSQC aliphatic
1322D CT 1H-13C HSQC aromatic
1423D 15N/13C-edited 1H-1H NOESY
152(4,3)D GFT (H)CCH-COSY aliphatic
162(4,3)D GFT (H)CCH-COSY aromatic
1723D (H)CCH-TOCSY
1823D HNCO
1923D HN(CA)CO
11023D HN(CA)CB
11123D CBCA(CO)NH
11223D HBHA(CO)NH
11312D CT 1H-13C HSQC aliphatic 28 ms
11413D 1H-15N TOCSY
11513D 1H-15N NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
1660 uM [U-5% 13C; U-15N] DA05R, 25 mM sodium phosphate, 50 mM sodium chloride, 0.02 % sodium azide, 1 mM protein inhibitor cocktail, 50 uM DSS, 90% H2O/10% D2O90% H2O/10% D2O
21 mM [U-13C; U-15N] DA05R, 25 mM sodium phosphate, 50 mM sodium chloride, 0.02 % sodium azide, 1 mM protein inhibitor cocktail, 50 uM DSS, 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
660 uMDA05R-1[U-5% 13C; U-15N]1
25 mMsodium phosphate-21
50 mMsodium chloride-31
0.02 %sodium azide-41
1 mMprotein inhibitor cocktail-51
50 uMDSS-61
1 mMDA05R-7[U-13C; U-15N]2
25 mMsodium phosphate-82
50 mMsodium chloride-92
0.02 %sodium azide-102
1 mMprotein inhibitor cocktail-112
50 uMDSS-122
Sample conditionspH: 6.5 / 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
PROSA6.4Guntertprocessing
AS-DP1Huang, Tejero, Powers and Montelionestructure solution
CNS1.3Brunger, Adams, Clore, Gros, Nilges and Readrefinement
CARA1.8.4Keller and Wuthrichdata analysis
CARA1.8.4Keller and Wuthrichpeak picking
CARA1.8.4Keller and Wuthrichchemical shift assignment
CYANA3Guntert, Mumenthaler and Wuthrichstructure solution
XEASY1.3.13Bartels et al.data analysis
VnmrJ4Variancollection
TALOS-NCornilescu, Delaglio and Baxgeometry optimization
PSVS1.5Bhattacharya and Montelionestructure validation
AutoAssign2.3.0Zimmerman, Moseley, Kulikowski and Montelionechemical shift assignment
CYANA3Guntert, Mumenthaler and Wuthrichrefinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR constraintsNOE constraints total: 1818 / NOE intraresidue total count: 407 / NOE long range total count: 563 / NOE medium range total count: 509 / NOE sequential total count: 339 / Protein chi angle constraints total count: 0 / Protein other angle constraints total count: 0 / Protein phi angle constraints total count: 67 / Protein psi angle constraints total count: 67
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 20

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