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- PDB-2klb: NMR Solution structure of a diflavin flavoprotein A3 from Nostoc ... -

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Basic information

Entry
Database: PDB / ID: 2klb
TitleNMR Solution structure of a diflavin flavoprotein A3 from Nostoc sp. PCC 7120, Northeast Structural Genomics Consortium Target NsR431C
ComponentsPutative diflavin flavoprotein A 3
KeywordsOXIDOREDUCTASE / PSI-2 / NESG / NsR431C / protein NMR / Q8YQD8 / Electron transport / Iron / Metal-binding / Transport / Structural Genomics / Protein Structure Initiative / Northeast Structural Genomics Consortium
Function / homology
Function and homology information


oxidoreductase activity, acting on the CH-NH group of donors, NAD or NADP as acceptor / Oxidoreductases / FMN binding / metal ion binding
Similarity search - Function
ODP domain / ODP family beta lactamase / Flavin reductase like domain / Flavin reductase like domain / Flavin reductase like domain / FMN-binding split barrel / Flavodoxin domain / Metallo-beta-lactamase superfamily / Metallo-beta-lactamase / Flavodoxin-like domain profile. ...ODP domain / ODP family beta lactamase / Flavin reductase like domain / Flavin reductase like domain / Flavin reductase like domain / FMN-binding split barrel / Flavodoxin domain / Metallo-beta-lactamase superfamily / Metallo-beta-lactamase / Flavodoxin-like domain profile. / Flavodoxin/nitric oxide synthase / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like / Flavoprotein-like superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Putative diflavin flavoprotein A 3
Similarity search - Component
Biological speciesNostoc sp. (bacteria)
MethodSOLUTION NMR / simulated annealing
Model detailslowest energy, model 1
AuthorsSwapna, G.V.T. / Ciccosanti, C. / Wang, D. / Jiang, M. / Xiao, R. / Acton, T.B. / Everett, J.K. / Nair, R. / Montelione, G.T. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published
Title: NMR Solution structure of a diflavin flavoprotein A3 from Nostoc sp. PCC 7120, Northeast Structural Genomics Consortium Target NsR431C
Authors: Swapna, G.V.T. / Ciccosanti, C. / Wang, D. / Jiang, M. / Xiao, R. / Acton, T.B. / Everett, J.K. / Nair, R. / Montelione, G.T.
History
DepositionJun 30, 2009Deposition site: BMRB / Processing site: RCSB
Revision 1.0Jul 21, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.2Feb 26, 2020Group: Data collection / Database references / Other
Category: pdbx_database_status / pdbx_nmr_spectrometer / struct_ref_seq_dif
Item: _pdbx_database_status.status_code_cs / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details
Revision 1.3Jun 14, 2023Group: Database references / Other / Category: database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data
Revision 1.4May 8, 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: Putative diflavin flavoprotein A 3


Theoretical massNumber of molelcules
Total (without water)16,4751
Polymers16,4751
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 / 140structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Putative diflavin flavoprotein A 3


Mass: 16475.482 Da / Num. of mol.: 1 / Fragment: Flavodoxin-like domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Nostoc sp. (bacteria) / Strain: PCC 7120 / Gene: all3895, dfa3 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) + Magic / References: UniProt: Q8YQD8

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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 CBCA(CO)NH
1413D HN(CA)CB
1513D HNCO
1613D HNCA
1713D HN(CO)CA
1813D HBHA(CO)NH
1913D 1H-13C NOESY
11013D 1H-15N NOESY
11132D 1H-15N HSQC
11232D 1H-13C HSQC
11322D 1H-15N HSQC
11422D 1H-13C HSQC
11523D 1H-13C NOESY
11613D (H)CCH-TOCSY
NMR detailsText: Data acquisition on B600 was performed using 35ul of 1.18mM sample and a 1.7mm microcryoprobe. The structure was determined using triple resonance NMR spectroscopy. Automated backbone ...Text: Data acquisition on B600 was performed using 35ul of 1.18mM sample and a 1.7mm microcryoprobe. The structure was determined using triple resonance NMR spectroscopy. Automated backbone assignments were made using AutoAssign. Sidechain assignments were completed manually. Automated NOESY assignments were made using AutoStructure and structure solution was determined using AutoStructure and CYANA-2.1. The structure calculations were done including the C-terminal 6xHis tag LEHHHHHH. Resonance assignments were validated using AVS validation software.

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Sample preparation

Details
Solution-IDContentsSolvent system
11.18 mM [U-100% 13C; U-100% 15N] NsR431C, 90% H2O/10% D2O90% H2O/10% D2O
21.18 mM [U-100% 13C; U-100% 15N] NsR431C 100% D2O100% D2O
31.18 mM [U-10% 13C; U-100% 15N] NsR431C, 100% D2O100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1.18 mMNsR431C-1[U-100% 13C; U-100% 15N]1
1.18 mMNsR431C-2[U-100% 13C; U-100% 15N]2
1.18 mMNsR431C-3[U-10% 13C; U-100% 15N]3
Sample conditionsIonic strength: 5mM CaCl2, 200mM NaCl / pH: 6.5 / Pressure: 1 atm / Temperature: 293 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE6001
Bruker AvanceBrukerAVANCE8002

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Processing

NMR software
NameVersionDeveloperClassification
AutoAssign2.2.1Zimmerman, Moseley, Kulikowski and Montelionechemical shift assignment
AutoAssign2.2.1Zimmerman, Moseley, Kulikowski and Montelionestructure solution
AutoStructure2.2.1Huang, Tejero, Powers and Montelionechemical shift assignment
AutoStructure2.2.1Huang, Tejero, Powers and Montelionestructure solution
CYANA2.1Guntert, Mumenthaler and Wuthrichgeometry optimization
CYANA2.1Guntert, Mumenthaler and Wuthrichstructure solution
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: 140 structures were calculated and 20 best conformers were refined in a shell of water using CNS. Initial dihedral angles were obtained using TALOS. Final quality scores were determined ...Details: 140 structures were calculated and 20 best conformers were refined in a shell of water using CNS. Initial dihedral angles were obtained using TALOS. Final quality scores were determined using PSVS software. Ordered residues are defined as: 2 - 9, 12 - 27, 31 - 36, 40 - 57, 61 - 79, 84 - 85, 87 - 89, 96 - 108, 110 - 111, 122 - 146; (a) RMSD (ordered residues) all Backbone atoms: 1.0A; all heavy atoms: 1.4A; (b) Ramachandran statistics for all ordered residues: Most favoured: 92.1%; Additionally allowed: 7.2%; Generously allowed: 0.6%; disallowed: 0.2%; (c) Procheck scores for ordered residues (Raw/Z)phi-psi -0.04/0.16, All:-0.10/-0.59. (d) MolProbity clash score (Raw/Z) 22.23/-2.12.
NMR constraintsNOE constraints total: 1672 / NOE intraresidue total count: 134 / NOE long range total count: 565 / NOE medium range total count: 481 / NOE sequential total count: 492
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 140 / Conformers submitted total number: 20 / Maximum lower distance constraint violation: 8.5 Å / Maximum upper distance constraint violation: 11.6 Å
NMR ensemble rmsDistance rms dev: 0.09 Å / Distance rms dev error: 0.09 Å

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