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Basic information

Entry
Database: PDB / ID: 2mlb
TitleNMR solution structure of a computational designed protein based on template of human erythrocytic ubiquitin
Componentsredesigned ubiquitin
KeywordsDE NOVO PROTEIN / protein design / Statistical energy Function / ubiquitin
Function / homologyPhosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / Ubiquitin-like (UB roll) / Roll / Alpha Beta
Function and homology information
Biological speciessynthetic (others)
MethodSOLUTION NMR / simulated annealing
Model detailsclosest to the average, model1
AuthorsXiong, P. / Wang, M. / Zhang, J. / Chen, Q. / Liu, H.
CitationJournal: Nat Commun / Year: 2014
Title: Protein design with a comprehensive statistical energy function and boosted by experimental selection for foldability
Authors: Xiong, P. / Wang, M. / Zhou, X. / Zhang, T. / Zhang, J. / Chen, Q. / Liu, H.
History
DepositionFeb 21, 2014Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Oct 29, 2014Provider: repository / Type: Initial release
Revision 1.1Sep 21, 2016Group: Database references
Revision 1.2Jun 14, 2023Group: Database references / Other / Category: database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data
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: redesigned ubiquitin


Theoretical massNumber of molelcules
Total (without water)8,5601
Polymers8,5601
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 / 1000structures with the lowest energy
RepresentativeModel #1closest to the average

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Components

#1: Protein redesigned ubiquitin


Mass: 8559.830 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic (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
1213D CBCA(CO)NH
1313D C(CO)NH
1413D HN(CA)CB
1513D HBHA(CO)NH
1613D H(CCO)NH
1723D (H)CCH-TOCSY
1813D 1H-15N NOESY
1923D 1H-13C NOESY
11023D (H)CCH-COSY

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Sample preparation

Details
Solution-IDContentsSolvent system
10.5-1 mM [U-100% 15N] redesigned ubiquitin-1, 25 mM phosphate buffer-2, 100 mM sodium chloride-3, 2 mM EDTA-4, 10 % [U-100% 2H] D2O-5, 90% H2O/10% D2O90% H2O/10% D2O
20.5-1 mM [U-100% 13C] redesigned ubiquitin-6, 25 mM phosphate buffer-7, 100 mM sodium chloride-8, 2 mM EDTA-9, 100 % [U-100% 2H] D2O-10, 100% D2O100% D2O
Sample
Conc. (mg/ml)UnitsComponentIsotopic labelingConc. range (mg/ml)Solution-ID
mMredesigned ubiquitin-1[U-100% 15N]0.5-11
25 mMphosphate buffer-21
100 mMsodium chloride-31
2 mMEDTA-41
10 %D2O-5[U-100% 2H]1
mMredesigned ubiquitin-6[U-100% 13C]0.5-12
25 mMphosphate buffer-72
100 mMsodium chloride-82
2 mMEDTA-92
100 %D2O-10[U-100% 2H]2
Sample conditionsIonic strength: 125 / pH: 6.5 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Bruker DMX / Manufacturer: Bruker / Model: DMX / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
CNS1.3Brunger, Adams, Clore, Gros, Nilges and Readgeometry optimization
CNS1.3Brunger, Adams, Clore, Gros, Nilges and Readrefinement
CNS1.3Brunger, Adams, Clore, Gros, Nilges and Readstructure solution
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 1000 / Conformers submitted total number: 20 / Representative conformer: 1

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