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- PDB-2kl3: Solution NMR structure of the Rhodanese-like domain from Anabaena... -

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Basic information

Entry
Database: PDB / ID: 2kl3
TitleSolution NMR structure of the Rhodanese-like domain from Anabaena sp Alr3790 protein. Northeast Structural Genomics Consortium Target NsR437A
ComponentsAlr3790 protein
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / alpha+beta / PSI-2 / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG
Function / homology
Function and homology information


Rhodanese-like domain / Oxidized Rhodanese; domain 1 / Rhodanese Homology Domain / Rhodanese-like domain / Rhodanese domain profile. / Rhodanese-like domain superfamily / Rhodanese-like domain / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesNostoc sp. (bacteria)
MethodSOLUTION NMR / simulated annealing
Model detailslowest energy, model 1
AuthorsEletsky, A. / Belote, R.L. / Ciccosanti, C. / Janjua, H. / Nair, R. / Rost, B. / Swapna, G.V.T. / Acton, T.B. / Xiao, R. / Everett, J.K. ...Eletsky, A. / Belote, R.L. / Ciccosanti, C. / Janjua, H. / Nair, R. / Rost, B. / Swapna, G.V.T. / Acton, T.B. / Xiao, R. / Everett, J.K. / Lee, H. / Prestegard, J.H. / Montelione, G.T. / Szyperski, T. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published
Title: Solution NMR structure of the Rhodanese-like domain from Anabaena sp Alr3790 protein. Northeast Structural Genomics Consortium Target NsR437A
Authors: Eletsky, A. / Belote, R.L. / Ciccosanti, C. / Janjua, H. / Nair, R. / Rost, B. / Swapna, G.V.T. / Acton, T.B. / Xiao, R. / Everett, J.K. / Lee, H. / Prestegard, J.H. / Montelione, G.T. / Szyperski, T.
History
DepositionJun 30, 2009Deposition site: BMRB / Processing site: RCSB
Revision 1.0Aug 11, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.2May 1, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_nmr_software / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Alr3790 protein


Theoretical massNumber of molelcules
Total (without water)14,5391
Polymers14,5391
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 Alr3790 protein


Mass: 14539.063 Da / Num. of mol.: 1
Fragment: Rhodanese-like domain sequence database residues 17-139
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Nostoc sp. (bacteria) / Strain: PCC 7120 / Gene: alr3790 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)+ Magic / References: UniProt: Q8YQN0

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1111D 15N T1
1211D 15N T2
1312D 1H-15N HSQC
1412D 1H-13C HSQC aliphatic
1512D 1H-13C CT-HSQC aliphatic
1612D 1H-13C CT-HSQC aromatic
1713D HNCO
1813D HN(CA)CO
1913D CBCA(CO)NH
11013D HN(CA)CB
11113D HBHA(CO)NH
11213D (H)CCH-TOCSY aliphatic
11313D (H)CCH-COSY aliphatic
11413D (H)CCH-COSY aromatic
11513D 1H-15N/13C NOESY
11622D 1H-15N HSQC long-range (His)
11722D 1H-13C CT-HSQC methyl
11822D 1H-15N HSQC
11922D 1H-15N TROSY
22032D 1H-15N HSQC
22132D 1H-15N TROSY
32242D 1H-15N HSQC
32342D 1H-15N TROSY
12412D CLEANEX

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Sample preparation

Details
Solution-IDContentsSolvent system
11 mM [U-100% 13C; U-100% 15N] nsr437a, 20 mM MES, 200 mM sodium chloride, 5 mM calcium chloride, 50 uM DSS, 0.02 % sodium azide, 90% H2O/10% D2O90% H2O/10% D2O
21 mM [U-2% 13C; U-100% 15N] nsr437a, 20 mM MES, 200 mM sodium chloride, 5 mM calcium chloride, 50 uM DSS, 0.02 % sodium azide, 90% H2O/10% D2O90% H2O/10% D2O
30.7 mM [U-2% 13C; U-100% 15N] nsr437a, 14.4 mM MES, 144 mM sodium chloride, 3.6 mM calcium chloride, 36 uM DSS, 0.014 % sodium azide, 13.25 g/l Pf1 phage, 87% H2O/13% D2O87% H2O/13% D2O
40.7 mM [U-2% 13C; U-100% 15N] nsr437a, 16 mM MES-21, 160 mM sodium chloride, 4 mM calcium chloride-23, 40 uM DSS, 0.016 % sodium azide, 4.2 % PEG, 88% H2O/12% D2O88% H2O/12% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMnsr437a-1[U-100% 13C; U-100% 15N]1
20 mMMES-21
200 mMsodium chloride-31
5 mMcalcium chloride-41
50 uMDSS-51
0.02 %sodium azide-61
1 mMnsr437a-7[U-2% 13C; U-100% 15N]2
20 mMMES-82
200 mMsodium chloride-92
5 mMcalcium chloride-102
50 uMDSS-112
0.02 %sodium azide-122
0.7 mMnsr437a-13[U-2% 13C; U-100% 15N]3
14.4 mMMES-143
144 mMsodium chloride-153
3.6 mMcalcium chloride-163
36 uMDSS-173
0.014 %sodium azide-183
13.25 mg/mLPf1 phage-193
0.7 mMnsr437a-20[U-2% 13C; U-100% 15N]4
16 mMMES-214
160 mMsodium chloride-224
4 mMcalcium chloride-234
40 uMDSS-244
0.016 %sodium azide-254
4.2 %PEG-264
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
1200 6.5 ambient 298 K
2150 6.5 ambient 298 K
3160 6.5 ambient 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA7501
Varian INOVAVarianINOVA6002
Varian INOVAVarianINOVA6003

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Processing

NMR software
NameVersionDeveloperClassification
VnmrJ2.1BVariancollection
PROSA6.4Guntertprocessing
CARA1.8.4Keller and Wuthrichdata analysis
CARA1.8.4Keller and Wuthrichpeak picking
CARA1.8.4Keller and Wuthrichchemical shift assignment
ANALYSIS2.0.7CCPNdata analysis
ANALYSIS2.0.7CCPNpeak picking
ANALYSIS2.0.7CCPNchemical shift assignment
PINEBahrami, Markley, Assadi, and Eghbalniachemical shift assignment
CYANA3Guntert, Mumenthaler and Wuthrichstructure solution
AutoStructureHuang, Tejero, Powers and Montelionestructure solution
TALOS2007.068.09.07Cornilescu, Delaglio and Baxdata analysis
CNS1.2.1Brunger, Adams, Clore, Gros, Nilges and Readrefinement
PSVS1.3Bhattacharya and Montelionevalidation
RefinementMethod: simulated annealing / Software ordinal: 1
Details: Structure determination was performed iteratively with CYANA and AUTOSTRUCTURE using NOE-based constraints, PHI and PSI dihedral angle constraints from TALOS, hydrogen bond constraints based ...Details: Structure determination was performed iteratively with CYANA and AUTOSTRUCTURE using NOE-based constraints, PHI and PSI dihedral angle constraints from TALOS, hydrogen bond constraints based on preliminary structures and CLEANEX data, and RDCs from two alignment media. The 20 conformers out of 100 with the lowest target function were further refined by simulated annealing in explicit water bath using the program CNS with PARAM19 force field.
NMR constraintsNOE constraints total: 2802 / NOE intraresidue total count: 517 / NOE long range total count: 978 / NOE medium range total count: 633 / NOE sequential total count: 674 / Hydrogen bond constraints total count: 220 / Protein chi angle constraints total count: 0 / Protein other angle constraints total count: 0 / Protein phi angle constraints total count: 64 / Protein psi angle constraints total count: 64
NMR representativeSelection criteria: lowest energy
NMR ensembleAverage torsion angle constraint violation: 0.12 ° / Conformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 20 / Maximum torsion angle constraint violation: 5.1 ° / Maximum upper distance constraint violation: 0.416 Å
NMR ensemble rmsDistance rms dev: 0.018 Å

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