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- PDB-2k5q: NMR Solution structure of membrane associated protein from Bacill... -

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Basic information

Entry
Database: PDB / ID: 2k5q
TitleNMR Solution structure of membrane associated protein from Bacillus cereus: Northeast Structural Genomics Consortium Target: BcR97A
ComponentsHypothetical Membrane Associated Protein BcR97A
KeywordsMEMBRANE PROTEIN / NESG / BcR97A / Bacillus cereus / Q812L6 protein / GFT NMR / Structural Genomics / PSI-2 / Protein Structure Initiative / Northeast Structural Genomics Consortium
Function / homologyProtein of unknown function DUF1093 / Protein of unknown function DUF1093 / YxeA-like superfamily / Protein of unknown function (DUF1093) / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Prokaryotic membrane lipoprotein lipid attachment site profile. / Beta Barrel / Mainly Beta / Hypothetical Membrane Associated Protein
Function and homology information
Biological speciesBacillus cereus ATCC 14579 (bacteria)
MethodSOLUTION NMR / simulated annealing
AuthorsSwapna, G. / Wang, D. / Owens, L. / Xiao, R. / Liu, J. / Baran, M.C. / Everett, J. / Acton, T.B. / Rost, B. / Montelione, G.T. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published
Title: NMR solution Structure of Membrane associated protein from Bacillus cereus: Northeast Structural Genomics Consortium Target: BcR97A
Authors: Swapna, G. / Wang, D.C. / Owens, L. / Xiao, R. / Liu, J. / Baran, M.C. / Everett, J. / Acton, T.B. / Rost, B. / Montelione, G.T.
History
DepositionJun 30, 2008Deposition site: BMRB / Processing site: RCSB
Revision 1.0Aug 26, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 16, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_spectrometer ...database_2 / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list / 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_spectrometer.model / _struct_ref_seq_dif.details
Revision 1.3May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Hypothetical Membrane Associated Protein BcR97A


Theoretical massNumber of molelcules
Total (without water)12,4581
Polymers12,4581
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 / 176structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Hypothetical Membrane Associated Protein BcR97A


Mass: 12458.083 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus cereus ATCC 14579 (bacteria) / Species: cereus / Gene: BC_4932 / Plasmid: pET 21-23C / Species (production host): coli / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)+MAGIC / References: UniProt: Q812L6

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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 HBHA(CO)NH
1713D C(CO)NH
1813D (H)CCH-TOCSY
1913D (H)CCH-COSY
11013D 13C-edited NOESY
11113D 1H-15N NOESY
11213D 13C-edited NOESY
21322D 1H-15N HSQC
21422D 1H-13C HSQC
NMR detailsText: GFT (4,3)D data was acquired for backbone assignments.

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Sample preparation

Details
Solution-IDContentsSolvent system
11.25 mM [U-100% 13C; U-100% 15N] BcR97A protein, 90% H2O/10% D2O90% H2O/10% D2O
20.77 mM [U-10% 13C; U-100% 15N] BcR97A protein, 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1.25 mMBcR97A protein[U-100% 13C; U-100% 15N]1
0.77 mMBcR97A protein[U-10% 13C; U-100% 15N]2
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
15mM CaCl2, 100mM NaCl 6.51 atm293 K
25mM CaCl2, 100mM NaCl 6.51 atm293 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA6001
Bruker AvanceBrukerAVANCE6002

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Processing

NMR software
NameVersionDeveloperClassification
AutoAssign2.2.1Zimmerman, Moseley, Kulikowski and Montelionechemical shift assignment
AutoStructure2.2.1Huang, Tejero, Powers and Montelionechemical shift assignment
AutoStructure2.2.1Huang, Tejero, Powers and Montelionestructure solution
CYANA2.1Guntert, Mumenthaler and Wuthrichstructure solution
CYANA2.1Guntert, Mumenthaler and Wuthrichgeometry optimization
CNS2.0.6Brunger, Adams, Clore, Gros, Nilges and Readrefinement
CNS2.0.6Brunger, Adams, Clore, Gros, Nilges and Readgeometry optimization
RefinementMethod: simulated annealing / Software ordinal: 1
Details: The structure was determined using triple resonance NMR spectroscopy. Automated backbone resonance assignments were made using AutoAssign and pattern picker algorithms developed for ...Details: The structure was determined using triple resonance NMR spectroscopy. Automated backbone resonance assignments were made using AutoAssign and pattern picker algorithms developed for automated assignments of GFT NMR data. Side chain assignments were completed manually. Automated NOESY assignments were made using AUTOSTRUCTURE and structure solution was determined using AUTOSTRUCTURE and CYANA-2.1. 176 structures were calculated and 20 best conformers were then refined in a shell of water using CNS. Initial Dihedral constriants were obtained from TALOS. The structure calculations were done including the C-terminal tag LEHHHHHH. Completeness of assignments excluding the 8-residue tag are: Backbone ~98.5%, sidechain ~ 95%, stereospecific methyl assignments 100%. The assignments were validated using the AVS software. Final structure quality factors determined using PSVS software: Ordered residues are defined as: 10-22,32-42,47-58,63-69,76-93. (a) RMSD(ordered residues) all Backbone atoms 0.9A; all heavy atoms 1.4A. (b) Ramachandran statistics for all ordered residues: Most favoured regions:85.9%, Additionally allowed regions 14.0%, Generously allowed region:0.2%. (c) Procheck scores for ordered residues (Raw/Z)phi-psi -0.73/-2.56, All:-0.49/-2.90 (d) MolProbity clash score (Raw/Z): 17.11/-1.41. (e) RPFscores for goodness of fit to NOESY data : Recall:0.963 Precision: 0.805F-measure:0.877 DP-score: 0.848
NMR constraintsNOE constraints total: 1121 / NOE intraresidue total count: 245 / NOE long range total count: 366 / NOE medium range total count: 129 / NOE sequential total count: 381 / Protein other angle constraints total count: 91 / Protein phi angle constraints total count: 51 / Protein psi angle constraints total count: 51
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 176 / Conformers submitted total number: 20 / Maximum upper distance constraint violation: 0.35 Å / Torsion angle constraint violation method: PSVS software
NMR ensemble rmsDistance rms dev: 0.01 Å

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