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- PDB-2m89: Solution structure of the Aha1 dimer from Colwellia psychrerythraea -

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Basic information

Entry
Database: PDB / ID: 2m89
TitleSolution structure of the Aha1 dimer from Colwellia psychrerythraea
ComponentsAha1 domain protein
KeywordsStructural Genomics / Unknown Function / domain dimer / hybrid methods / Rosetta / PSI-biology / Northeast Structural Genomics Consortium / NESG
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 / Aha1 domain protein
Function and homology information
Biological speciesColwellia psychrerythraea (bacteria)
MethodSOLUTION NMR / SOLUTION SCATTERING / torsion angle dynamics
Model detailsstructural features, model1
AuthorsRossi, P. / Sgourakis, N.G. / Shi, L. / Liu, G. / Barbieri, C.M. / Lee, H. / Grant, T.D. / Luft, J.R. / Xiao, R. / Acton, T.B. ...Rossi, P. / Sgourakis, N.G. / Shi, L. / Liu, G. / Barbieri, C.M. / Lee, H. / Grant, T.D. / Luft, J.R. / Xiao, R. / Acton, T.B. / Montelione, G.T. / Snell, E.H. / Baker, D. / Lange, O.A. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: Proteins / Year: 2015
Title: A hybrid NMR/SAXS-based approach for discriminating oligomeric protein interfaces using Rosetta.
Authors: Rossi, P. / Shi, L. / Liu, G. / Barbieri, C.M. / Lee, H.W. / Grant, T.D. / Luft, J.R. / Xiao, R. / Acton, T.B. / Snell, E.H. / Montelione, G.T. / Baker, D. / Lange, O.F. / Sgourakis, N.G.
History
DepositionMay 9, 2013Deposition site: BMRB / Processing site: RCSB
Revision 1.0Sep 4, 2013Provider: repository / Type: Initial release
Revision 1.1Dec 10, 2014Group: Database references
Revision 1.2Feb 4, 2015Group: Database references
Revision 1.3Apr 27, 2016Group: Structure summary
Revision 1.4May 1, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Aha1 domain protein
B: Aha1 domain protein


Theoretical massNumber of molelcules
Total (without water)33,4882
Polymers33,4882
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)10 / 40000target function
RepresentativeModel #1structural features

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Components

#1: Protein Aha1 domain protein


Mass: 16743.947 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Colwellia psychrerythraea (bacteria) / Strain: 34H / ATCC BAA-681 / Gene: CPS_1688 / Production host: Escherichia coli (E. coli) / References: UniProt: Q484T9

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Experimental details

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Experiment

Experiment
Method
SOLUTION NMR
SOLUTION SCATTERING
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1222D 1H-15N HSQC
1332D 1H-15N HSQC
1442D 1H-15N HSQC
1522D 1H-1H TOCSY
1612D 1H-1H NOESY
1712D 1H-13C HSQC aromatic
1812D 1H-13C HSQC aliphatic
1932D 1H-13C HSQC aliphatic
11023D HNCO

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Sample preparation

Details
Solution-IDContentsSolvent system
11.3 mM [U-100% 13C; U-100% 15N] protein, 90% H2O/10% D2O90% H2O/10% D2O
20.7 mM [U-2H,13C,15N]; Ile 1-[13CH3]; Leu,Val-[13CH3] protein, 90% H2O/10% D2O90% H2O/10% D2O
31.1 mM [U-5%-13C,100%-15N] protein, 90% H2O/10% D2O90% H2O/10% D2O
41.1 mM [U-5%-13C,100%-15N] protein, 12.5 mg/mL Pf1 phage, 90% H2O/10% D2O90% H2O/10% D2O
51.1 mM [U-5%-13C,100%-15N] protein, 4.0 % PEG(C5E12), 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1.3 mMentity-1[U-100% 13C; U-100% 15N]1
0.7 mMentity-2[U-2H,13C,15N]; Ile 1-[13CH3]; Leu,Val-[13CH3]2
1.1 mMentity-3[U-5%-13C,100%-15N]3
1.1 mMentity-4[U-5%-13C,100%-15N]4
12.5 mg/mLPf1 phage-54
1.1 mMentity-6[U-5%-13C,100%-15N]5
4.0 %PEG(C5E12)-75
Sample conditionsIonic strength: 100 / pH: 7.5 / Pressure: ambient / Temperature: 298 K

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Data collection

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

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Processing

NMR software
NameVersionDeveloperClassification
TopSpin2.1Brukercollection
TopSpin2.1Brukerprocessing
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
SparkyGoddardchemical shift assignment
CYANAGuntert, Mumenthaler and Wuthrichdata analysis
CS-ROSETTAShen, Vernon, Baker and Baxstructure solution
PSVSBhattacharya and Montelionestructure validation
CS-ROSETTArefinement
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR constraintsNOE constraints total: 1483 / NOE intraresidue total count: 0 / NOE long range total count: 1483 / NOE medium range total count: 0 / NOE sequential total count: 0 / Protein chi angle constraints total count: 0 / Protein other angle constraints total count: 0 / Protein phi angle constraints total count: 0 / Protein psi angle constraints total count: 0
NMR representativeSelection criteria: structural features
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 40000 / Conformers submitted total number: 10 / Maximum lower distance constraint violation: 0 Å / Maximum upper distance constraint violation: 0.49 Å
NMR ensemble rmsDistance rms dev: 0.14 Å

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