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- PDB-2luz: Solution NMR Structure of CalU16 from Micromonospora echinospora,... -

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Basic information

Entry
Database: PDB / ID: 2luz
TitleSolution NMR Structure of CalU16 from Micromonospora echinospora, Northeast Structural Genomics Consortium (NESG) Target MiR12
ComponentsCalU16
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / NORTHEAST STRUCTURAL GENOMICS CONSORTIUM / NESG / PSI-Biology / Protein Structure Initiative / Enzyme Discovery for Natural Product Biosynthesis / NatPro
Function / homologyActivator of Hsp90 ATPase homologue 1-like / Activator of Hsp90 ATPase homolog 1-like protein / START domain / Alpha-D-Glucose-1,6-Bisphosphate; Chain A, domain 4 / START-like domain superfamily / 2-Layer Sandwich / Alpha Beta / CalU16
Function and homology information
Biological speciesMicromonospora echinospora (bacteria)
MethodSOLUTION NMR / simulated annealing
Model detailslowest energy, model 1
AuthorsRamelot, T.A. / Yang, Y. / Lee, H. / Pederson, K. / Lee, D. / Kohan, E. / Janjua, H. / Xiao, R. / Acton, T.B. / Everett, J.K. ...Ramelot, T.A. / Yang, Y. / Lee, H. / Pederson, K. / Lee, D. / Kohan, E. / Janjua, H. / Xiao, R. / Acton, T.B. / Everett, J.K. / Wrobel, R.L. / Bingman, C.A. / Singh, S. / Thorson, J.S. / Prestegard, J.H. / Montelione, G.T. / Phillips Jr., G.N. / Kennedy, M.A. / Enzyme Discovery for Natural Product Biosynthesis (NatPro) / Northeast Structural Genomics Consortium (NESG)
CitationJournal: Acs Chem.Biol. / Year: 2014
Title: Structure-Guided Functional Characterization of Enediyne Self-Sacrifice Resistance Proteins, CalU16 and CalU19.
Authors: Elshahawi, S.I. / Ramelot, T.A. / Seetharaman, J. / Chen, J. / Singh, S. / Yang, Y. / Pederson, K. / Kharel, M.K. / Xiao, R. / Lew, S. / Yennamalli, R.M. / Miller, M.D. / Wang, F. / Tong, L. ...Authors: Elshahawi, S.I. / Ramelot, T.A. / Seetharaman, J. / Chen, J. / Singh, S. / Yang, Y. / Pederson, K. / Kharel, M.K. / Xiao, R. / Lew, S. / Yennamalli, R.M. / Miller, M.D. / Wang, F. / Tong, L. / Montelione, G.T. / Kennedy, M.A. / Bingman, C.A. / Zhu, H. / Phillips, G.N. / Thorson, J.S.
History
DepositionJun 22, 2012Deposition site: BMRB / Processing site: RCSB
Revision 1.0Oct 3, 2012Provider: repository / Type: Initial release
Revision 1.1Oct 9, 2013Group: Structure summary
Revision 1.2Nov 12, 2014Group: Database references
Revision 1.3Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer / struct_ref_seq_dif
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 / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details
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: CalU16


Theoretical massNumber of molelcules
Total (without water)21,3751
Polymers21,3751
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 CalU16


Mass: 21374.805 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Micromonospora echinospora (bacteria) / Gene: calU16 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pMgK / References: UniProt: Q8KNE9

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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 1H-13C NOESY aliphatic
1713D 1H-13C NOESY aromatic
1813D (H)CCH-TOCSY
1923D (H)CCH-TOCSY
11042D 1H-13C HSQC
11124D CC-NOESY
11213D HBHA(CO)NH
11313D (H)CCH-COSY
11413D C(CO)NH
11513D H(CCO)NH
1163NUS 3D 1H-13C NOESY aliphatic
1173NUS 3D 1H-15N NOESY
11813D 1H-15N NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
10.9 mM [U-100% 13C; U-100% 15N] mir12.006, 0.02 % NaN3, 10 mM DTT, 5 mM CaCL2, 100 mM NaCL, 1 x Proteinase Inhibitors, 20 mM MES pH 6.5, 10 % D2O, 50 uM DSS, 90% H2O/10% D2O90% H2O/10% D2O
20.9 mM [U-100% 13C; U-100% 15N] mir12.006, 0.02 % NaN3, 10 mM DTT, 5 mM CaCL2, 100 mM NaCL, 1 x Proteinase Inhibitors, 20 mM MES pH 6.5, 100 % D2O, 50 uM DSS, 100% D2O100% D2O
30.9 mM [U-100% 13C; U-100% 15N] mir12.011, 0.02 % NaN3, 10 mM DTT, 5 mM CaCL2, 100 mM NaCL, 1 x Proteinase Inhibitors, 20 mM MES pH 6.5, 10 % D2O, 50 uM DSS, 90% H2O/10% D2O90% H2O/10% D2O
40.9 mM [U-100% 15N], 5% 13C stereo mir12.008, 0.02 % NaN3, 10 mM DTT, 5 mM CaCL2, 100 mM NaCL, 1 x Proteinase Inhibitors, 20 mM MES pH 6.5, 10 % D2O, 50 uM DSS, 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.9 mMmir12.006-1[U-100% 13C; U-100% 15N]1
0.02 %NaN3-21
10 mMDTT-31
5 mMCaCL2-41
100 mMNaCL-51
1 %Proteinase Inhibitors-61
20 mMMES pH 6.5-71
10 %D2O-81
50 uMDSS-91
0.9 mMmir12.006-10[U-100% 13C; U-100% 15N]2
0.02 %NaN3-112
10 mMDTT-122
5 mMCaCL2-132
100 mMNaCL-142
1 %Proteinase Inhibitors-152
20 mMMES pH 6.5-162
100 %D2O-172
50 uMDSS-182
0.9 mMmir12.011-19[U-100% 13C; U-100% 15N]3
0.02 %NaN3-203
10 mMDTT-213
5 mMCaCL2-223
100 mMNaCL-233
1 %Proteinase Inhibitors-243
20 mMMES pH 6.5-253
10 %D2O-263
50 uMDSS-273
0.9 mMmir12.008-28[U-100% 15N], 5% 13C stereo4
0.02 %NaN3-294
10 mMDTT-304
5 mMCaCL2-314
100 mMNaCL-324
1 %Proteinase Inhibitors-334
20 mMMES pH 6.5-344
10 %D2O-354
50 uMDSS-364
Sample conditionspH: 6.5 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE8001
Varian INOVAVarianINOVA6002
Bruker AvanceIIIBrukerAVANCE III6003

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Processing

NMR software
NameVersionDeveloperClassification
CNS1.3Brunger, Adams, Clore, Gros, Nilges and Readrefinement
CNS1.3Brunger, Adams, Clore, Gros, Nilges and Readstructure solution
CNS1.3Brunger, Adams, Clore, Gros, Nilges and Readgeometry optimization
CYANA3Guntert, Mumenthaler and Wuthrichrefinement
CYANA3Guntert, Mumenthaler and Wuthrichgeometry optimization
CYANA3Guntert, Mumenthaler and Wuthrichstructure solution
AutoStructureASDP-1.0Huang, Tejero, Powers and Montelionedata analysis
AutoStructureASDP-1.0Huang, Tejero, Powers and Montelionerefinement
NMRPipe2008 linux9Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
TopSpin2.1.4 and 3.1Bruker Biospincollection
VnmrJ1.1 DVariancollection
PINEBahrami, Markley, Assadi, and Eghbalniachemical shift assignment
Sparky3.113Goddarddata analysis
TALOS+Shen, Cornilescu, Delaglio and Baxgeometry optimization
PALESPALES (Zweckstetter, Bax)geometry optimization
PSVS1.5Bhattacharya, Montelionestructure validation
FMCGUIAlex Lemak, Cheryl Arrowsmith, University of Torontorefinement
RefinementMethod: simulated annealing / Software ordinal: 1 / Details: CNS WATER REFINEMENT
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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