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- PDB-2ldk: Solution NMR Structure of Protein AAur_3427 from Arthrobacter aur... -

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Basic information

Entry
Database: PDB / ID: 2ldk
TitleSolution NMR Structure of Protein AAur_3427 from Arthrobacter aurescens, Northeast Structural Genomics Consortium Target AaR96
ComponentsUncharacterized protein
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / NORTHEAST STRUCTURAL GENOMICS CONSORTIUM (NESG) / PSI-Biology / Protein Structure Initiative
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 / Uncharacterized protein
Function and homology information
Biological speciesArthrobacter aurescens (bacteria)
MethodSOLUTION NMR / simulated annealing
Model detailslowest energy, model 1
AuthorsEletsky, A. / Lee, H. / Wang, D. / Ciccosanti, C. / Janjua, H. / Nair, R. / Rost, B. / Acton, T.B. / Xiao, R. / Everett, J.K. ...Eletsky, A. / Lee, H. / Wang, D. / Ciccosanti, C. / Janjua, H. / Nair, R. / Rost, B. / Acton, T.B. / Xiao, R. / Everett, J.K. / Prestegard, J.H. / Montelione, G.T. / Szyperski, T. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published
Title: Solution NMR Structure of Protein AAur_3427 from Arthrobacter aurescens, Northeast Structural Genomics Consortium Target AaR96
Authors: Eletsky, A. / Lee, H. / Wang, D. / Ciccosanti, C. / Janjua, H. / Nair, R. / Rost, B. / Acton, T.B. / Xiao, R. / Everett, J.K. / Prestegard, J.H. / Montelione, G.T. / Szyperski, T.
History
DepositionMay 27, 2011Deposition site: BMRB / Processing site: RCSB
Revision 1.0Jun 22, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 22, 2012Group: Structure summary
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: Uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)19,6261
Polymers19,6261
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 Uncharacterized protein


Mass: 19625.697 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arthrobacter aurescens (bacteria) / Strain: TC1 / Gene: AAur_3427 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)+ Magic / References: UniProt: A1RA60

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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 CT-HSQC aliphatic
1313D HNCO
1413D CBCA(CO)NH
1513D HN(CA)CB
1612D 1H-13C CT-HSQC aromatic
1713D simutaneous 13C-aromatic,13C-aliphatic,15N edited 1H-1H NOESY
1813D (H)CCH-TOCSY aliphatic
1913D HBHA(CO)NH
11013D HN(CA)CO
11112D 1H-15N LR-HSQC histidine
11212D (HB)CB(CGCDCE)HDHE
1131(4,3)D GFT (H)CCH-COSY aliphatic
11413D (H)CCH-COSY aromatic
11522D 1H-13C CT-HSQC methyl
11611D 15N T1
11711D 15N T2
11822D J-mod 1H-15N HSQC
11932D J-mod 1H-15N HSQC
12042D J-mod 1H-15N HSQC

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Sample preparation

Details
Solution-IDContentsSolvent system
10.6 mM [U-100% 13C; U-100% 15N] AaR96, 20 mM MES, 100 mM sodium chloride, 5 mM calcium chloride, 10 mM DTT, 50 uM DSS, 0.02 % sodium azide, 90% H2O/10% D2O90% H2O/10% D2O
21.7 mM [5% 13C; U-100% 15N] AaR96, 20 mM MES, 100 mM sodium chloride, 5 mM calcium chloride, 10 mM DTT, 50 uM DSS, 0.02 % sodium azide, 90% H2O/10% D2O90% H2O/10% D2O
31.2 mM [5% 13C; U-100% 15N] AaR96, 20 mM MES, 100 mM sodium chloride, 5 mM calcium chloride, 10 mM DTT, 50 uM DSS, 0.02 % sodium azide, 4 % C12E5 PEG, 1.3 % hexanol, 80% H2O/20% D2O80% H2O/20% D2O
41.1 mM [5% 13C; U-100% 15N] AaR96, 13 mM MES, 70 mM sodium chloride, 3 mM calcium chloride, 10 mM DTT, 33 uM DSS, 0.02 % sodium azide, 12.5 g/l Pf1 phage, 80% H2O/20% D2O80% H2O/20% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.6 mMAaR96-1[U-100% 13C; U-100% 15N]1
20 mMMES-21
100 mMsodium chloride-31
5 mMcalcium chloride-41
10 mMDTT-51
50 uMDSS-61
0.02 %sodium azide-71
1.7 mMAaR96-8[5% 13C; U-100% 15N]2
20 mMMES-92
100 mMsodium chloride-102
5 mMcalcium chloride-112
10 mMDTT-122
50 uMDSS-132
0.02 %sodium azide-142
1.2 mMAaR96-15[5% 13C; U-100% 15N]3
20 mMMES-163
100 mMsodium chloride-173
5 mMcalcium chloride-183
10 mMDTT-193
50 uMDSS-203
0.02 %sodium azide-213
4 %C12E5 PEG-223
1.3 %hexanol-233
1.1 mMAaR96-24[5% 13C; U-100% 15N]4
13 mMMES-254
70 mMsodium chloride-264
3 mMcalcium chloride-274
10 mMDTT-284
33 uMDSS-294
0.02 %sodium azide-304
12.5 mg/mLPf1 phage-314
Sample conditionspH: 6.5 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE9001
Varian INOVAVarianINOVA6002
Varian INOVAVarianINOVA7503
Varian INOVAVarianINOVA6004
Bruker AvanceBrukerAVANCE7005

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Processing

NMR software
NameVersionDeveloperClassification
CNS1.2Brunger, Adams, Clore, Gros, Nilges and Readrefinement
CNS1.2Brunger, Adams, Clore, Gros, Nilges and Readstructure solution
CNS1.2Brunger, Adams, Clore, Gros, Nilges and Readgeometry optimization
CYANA3Guntert, Mumenthaler and Wuthrichrefinement
CYANA3Guntert, Mumenthaler and Wuthrichgeometry optimization
CYANA3Guntert, Mumenthaler and Wuthrichstructure solution
AutoStructure2.2.1Huang, Tejero, Powers and Montelionedata analysis
AutoStructure2.2.1Huang, Tejero, Powers and Montelionerefinement
AutoAssign2.3.0Zimmerman, Moseley, Kulikowski and Montelionedata analysis
AutoAssign2.3.0Zimmerman, Moseley, Kulikowski and Montelionechemical shift assignment
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
XEASY1.3.13Bartels et al.data analysis
TopSpin2.1Bruker Biospincollection
TopSpin2.1Bruker Biospinprocessing
VnmrJ2.2DVariancollection
TALOS+1.2009.0721.18Shen, Cornilescu, Delaglio and Baxgeometry optimization
CARA1.8.4Keller and Wuthrichdata analysis
CARA1.8.4Keller and Wuthrichchemical shift assignment
CARA1.8.4Keller and Wuthrichpeak picking
PROSA6.4Guntertprocessing
CNSBrunger, Adams, Clore, Gros, Nilges and Readrefinement
RefinementMethod: simulated annealing / Software ordinal: 1
Details: Structure determination was performed by running CYANA and AUTOSTRUCTURE in parallel using NOE-based constraints and PHI and PSI dihedral angle constraints from TALOS+. Consensus peak ...Details: Structure determination was performed by running CYANA and AUTOSTRUCTURE in parallel using NOE-based constraints and PHI and PSI dihedral angle constraints from TALOS+. Consensus peak assignments were selected and used in iterative refinement with CYANA, with RDC constraints added at later stages. 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: 4542 / NOE intraresidue total count: 523 / NOE long range total count: 1862 / NOE medium range total count: 1031 / NOE sequential total count: 1126 / Protein chi angle constraints total count: 0 / Protein other angle constraints total count: 0 / Protein phi angle constraints total count: 74 / Protein psi angle constraints total count: 74
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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