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- PDB-2n8i: Solution NMR Structure of Designed Protein DA05, Northeast Struct... -

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Basic information

Entry
Database: PDB / ID: 2n8i
TitleSolution NMR Structure of Designed Protein DA05, Northeast Structural Genomics Consortium (NESG) Target OR626
ComponentsDesigned Protein DA05Design
KeywordsDE NOVO PROTEIN / designed protein / PSI-Biology / Northeast Structural Genomics Consortium / NESG
Biological speciessynthetic construct (others)
MethodSOLUTION NMR / simulated annealing
Model detailslowest energy, model1
AuthorsXu, X. / Eletsky, A. / Federizon, J.F. / 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 15, 2015Deposition site: BMRB / Processing site: RCSB
Revision 1.0Jan 20, 2016Provider: repository / Type: Initial release
Revision 1.1Jan 27, 2016Group: Structure summary
Revision 1.2May 18, 2016Group: Database references
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: Designed Protein DA05


Theoretical massNumber of molelcules
Total (without water)11,1491
Polymers11,1491
Non-polymers00
Water0
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 DA05 / Design


Mass: 11148.562 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
1112D 1H-15N HSQC
1212D CT 1H-13C HSQC aliphatic
1312D CT 1H-13C HSQC aromatic
1413D 15N/13C-edited 1H-1H NOESY
151(4,3)D GFT (H)CCH-COSY aliphatic
161(4,3)D GFT (H)CCH-COSY aromatic
171(4,3)D GFT HNNCACBCA
1813D (H)CCH-TOCSY
1913D HNCO
11013D HN(CA)CO
1111(4,3)D GFT CABCA(CO)NHN
11222D CT 1H-13C HSQC aliphatic 28 ms
11322D CT 1H-13C HSQC aliphatic 42 ms
11422D CT 1H-13C HSQC aliphatic 56 ms

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Sample preparation

Details
Solution-IDContentsSolvent system
1600 uM [U-13C; U-15N] DA05, 25 mM sodium phosphate, 50 mM sodium chloride, 0.02 % sodium azide, 0.5 mM PMSF, 50 uM DSS, 90% H2O/10% D2O90% H2O/10% D2O
2200 uM [U-5% 13C; U-15N] DA05, 25 mM sodium phosphate, 50 mM sodium chloride, 0.02 % sodium azide, 0.5 mM PMSF, 50 uM DSS, 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
600 uMDA05-1[U-13C; U-15N]1
25 mMsodium phosphate-21
50 mMsodium chloride-31
0.02 %sodium azide-41
0.5 mMPMSF-51
50 uMDSS-61
200 uMDA05-7[U-5% 13C; U-15N]2
25 mMsodium phosphate-82
50 mMsodium chloride-92
0.02 %sodium azide-102
0.5 mMPMSF-112
50 uMDSS-122
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
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: 1506 / NOE intraresidue total count: 452 / NOE long range total count: 330 / NOE medium range total count: 396 / NOE sequential total count: 328 / Protein chi angle constraints total count: 0 / Protein other angle constraints total count: 0 / Protein phi angle constraints total count: 77 / Protein psi angle constraints total count: 77
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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