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- PDB-2lf2: Solution NMR structure of the AHSA1-like protein CHU_1110 from Cy... -

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Basic information

Entry
Database: PDB / ID: 2lf2
TitleSolution NMR structure of the AHSA1-like protein CHU_1110 from Cytophaga hutchinsonii, Northeast Structural Genomics Consortium Target ChR152
ComponentsUncharacterized protein
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / NESG / PSI-Biology / Protein Structure Initiative / Northeast Structural Genomics Consortium
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 / Activator of Hsp90 ATPase homologue 1/2-like C-terminal domain-containing protein / Uncharacterized protein
Function and homology information
Biological speciesCytophaga hutchinsonii (bacteria)
MethodSOLUTION NMR / simulated annealing
Model detailslowest energy, model 1
AuthorsYang, Y. / Ramelot, T.A. / Lee, D. / Ciccosanti, C. / Acton, T.B. / Xiao, R. / Everett, J.K. / Montelione, G.T. / Kennedy, M.A. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published
Title: Solution NMR structure of the AHSA1-like protein CHU_1110 from Cytophaga hutchinsonii, Northeast Structural Genomics Consortium Target ChR152.
Authors: Yang, Y. / Ramelot, T.A. / Lee, D. / Ciccosanti, C. / Acton, T.B. / Xiao, R. / Everett, J.K. / Montelione, G.T. / Kennedy, M.A.
History
DepositionJun 28, 2011Deposition site: BMRB / Processing site: RCSB
Revision 1.0Jul 13, 2011Provider: repository / Type: Initial release
Revision 1.1Feb 22, 2012Group: Structure summary
Revision 1.2Jun 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 1.3May 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

Downloads & links

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Assembly

Deposited unit
A: Uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)20,3331
Polymers20,3331
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 / 150structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Uncharacterized protein


Mass: 20333.123 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Cytophaga hutchinsonii (bacteria) / Strain: ATCC 33406 / NCIMB 9469 / Gene: CHU_1110 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) pMGK / References: UniProt: Q11W30, UniProt: A0A6N4SQ07*PLUS

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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 aliphatic
1312D 1H-13C HSQC aromatic
1432D 1H-15N HSQC
1532D 1H-13C HSQC
1622D 1H-13C HSQC-CT
1723D 1H-15N NOESY
1813D 1H-13C NOESY aliph
1913D HNCO
11013D HN(CA)CB
11113D CBCA(CO)NH
11213D HNCA
11313D HN(CO)CA
11413D HBHA(CO)NH
11513D H(CCO)NH
11613D C(CCO)NH
11713D (H)CCH-COSY
11813D (H)CCH-TOCSY
11933D CCH-TOCSY
12034D CC-NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
11.05 mM [U-100% 13C; U-100% 15N] AHSA1-like protein CHU_1110 from Cytophaga hutchinsonii, 10 mM Tris-HCl, 100 mM sodium chloride, 0.02 % sodium azide, 5 mM DTT, 90% H2O/10% D2O90% H2O/10% D2O
21.07 mM [U-5% 13C; U-100% 15N] AHSA1-like protein CHU_1110 from Cytophaga hutchinsonii, 10 mM Tris-HCl, 100 mM sodium chloride, 10 mM DTT, 0.02 % sodium azide, 90% H2O/10% D2O90% H2O/10% D2O
31.05 mM [U-100% 13C; U-100% 15N] AHSA1-like protein CHU_1110 from Cytophaga hutchinsonii, 10 mM Tris-HCl, 100 mM sodium chloride, 0.02 % sodium azide, 10 mM DTT, 100% D2O100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1.05 mMAHSA1-like protein CHU_1110 from Cytophaga hutchinsonii-1[U-100% 13C; U-100% 15N]1
10 mMTris-HCl-21
100 mMsodium chloride-31
0.02 %sodium azide-41
5 mMDTT-51
1.07 mMAHSA1-like protein CHU_1110 from Cytophaga hutchinsonii-6[U-5% 13C; U-100% 15N]2
10 mMTris-HCl-72
100 mMsodium chloride-82
10 mMDTT-92
0.02 %sodium azide-102
1.05 mMAHSA1-like protein CHU_1110 from Cytophaga hutchinsonii-11[U-100% 13C; U-100% 15N]3
10 mMTris-HCl-123
100 mMsodium chloride-133
0.02 %sodium azide-143
10 mMDTT-153
Sample conditionsIonic strength: 0.2 / pH: 7.5 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA6001
Bruker Avance IIIBrukerAVANCE III8502

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Processing

NMR software
NameVersionDeveloperClassification
NMRPipe2008Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
VNMR6.1CVariancollection
TopSpin2.1.4Bruker Biospincollection
AutoStructure2.2.1Huang, Tejero, Powers and Montelionedata analysis
X-PLOR NIH2.25Schwieters, Kuszewski, Tjandra and Clorestructure solution
CNS1.2Brunger, Adams, Clore, Gros, Nilges and Readrefinement
Sparky3.113Goddarddata analysis
PSVS1.4Bhattacharya and Montelionerefinement
AutoAssign2.3Zimmerman, Moseley, Kulikowski and Montelionechemical shift assignment
PdbStat5.1(PdbStat)-Roberto Tejero and Gaetano T. Montelionestructure solution
PINE Server1Bahrami, Markley, Assadi, and Eghbalniachemical shift autoassignment
CYANA2.1Guntert, Mumenthaler and Wuthrichstructure solution
X-PLOR_NIH_with_HBDBSchwieters, Kuszewski, Tjandra and Clorerefinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR constraintsNOE constraints total: 1901 / NOE intraresidue total count: 529 / NOE long range total count: 648 / NOE medium range total count: 246 / NOE sequential total count: 478 / Hydrogen bond constraints total count: 166
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 150 / Conformers submitted total number: 20

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