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- PDB-2ksc: Solution structure of Synechococcus sp. PCC 7002 hemoglobin -

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Basic information

Entry
Database: PDB / ID: 2ksc
TitleSolution structure of Synechococcus sp. PCC 7002 hemoglobin
ComponentsCyanoglobin
KeywordsUNKNOWN FUNCTION / hemeprotein / 2/2 hemoglobin / GlbN / trHbN
Function / homology
Function and homology information


oxygen carrier activity / oxygen binding / heme binding / metal ion binding
Similarity search - Function
Truncated hemoglobin, group 1 / Truncated hemoglobin / Bacterial-like globin / Globin/Protoglobin / Globins / Globin-like / Globin-like superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
HEME B/C / Group 1 truncated hemoglobin
Similarity search - Component
Biological speciesSynechococcus sp. (bacteria)
MethodSOLUTION NMR / DGSA-distance geometry simulated annealing, torsion angle dynamics
Model detailsminimized average, model 1
Model type detailsminimized average
AuthorsVuletich, D.A. / Falzone, C.J. / Lecomte, J.T.J.
Citation
Journal: Biochemistry / Year: 2010
Title: Functional and structural characterization of the 2/2 hemoglobin from Synechococcus sp. PCC 7002.
Authors: Scott, N.L. / Xu, Y. / Shen, G. / Vuletich, D.A. / Falzone, C.J. / Li, Z. / Ludwig, M. / Pond, M.P. / Preimesberger, M.R. / Bryant, D.A. / Lecomte, J.T.
#1: Journal: BIOMOL.NMR ASSIGN. / Year: 2009
Title: (1)H, (15)N, and (13)C resonance assignments of the 2/2 hemoglobin from the cyanobacterium Synechococcus sp. PCC 7002 in the ferric bis-histidine state
Authors: Pond, M.P. / Vuletich, D.A. / Falzone, C.J. / Majumdar, A. / Lecomte, J.T.J.
History
DepositionJan 2, 2010Deposition site: BMRB / Processing site: RCSB
Revision 1.0Feb 9, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 26, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / struct_conn
Item: _pdbx_database_status.status_code_cs / _pdbx_nmr_software.name / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cyanoglobin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,3612
Polymers13,7421
Non-polymers6191
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)16 / 30structures with the least restraint violations
RepresentativeModel #1minimized average

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Components

#1: Protein Cyanoglobin


Mass: 13742.418 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Synechococcus sp. (bacteria) / Strain: PCC 7002 / Gene: glbN, SYNPCC7002_A1621 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q8RT58
#2: Chemical ChemComp-HEB / HEME B/C / HYBRID BETWEEN B AND C TYPE HEMES (PROTOPORPHYRIN IX CONTAINING FE)


Mass: 618.503 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H34FeN4O4

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1133D 1H-15N NOESY
1243D 1H-13C NOESY
1312D 1H-1H NOESY
1422D 1H-1H NOESY
1533D HNHA

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Sample preparation

Details
Solution-IDContentsSolvent system
11-2 mM holoprotein, 90% H2O/10% D2O90% H2O/10% D2O
21-4 mM holoprotein, 100% D2O100% D2O
31-2 mM [U-100% 15N] holoprotein, 90% H2O/10% D2O90% H2O/10% D2O
40.6-1.4 mM [U-100% 13C; U-100% 15N] holoprotein, 90% H2O/10% D2O90% H2O/10% D2O
Sample
UnitsComponentIsotopic labelingConc. range (mg/ml)Solution-ID
mMholoprotein-11-21
mMholoprotein-21-42
mMholoprotein-3[U-100% 15N]1-23
mMholoprotein-4[U-100% 13C; U-100% 15N]0.6-1.44
Sample conditionsIonic strength: 0.025 / pH: 7.2 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Bruker DRX / Manufacturer: Bruker / Model: DRX / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
X-PLOR NIH2.23Schwieters, Kuszewski, Tjandra and Clorestructure solution
X-PLOR NIH2.23Schwieters, Kuszewski, Tjandra and Clorerefinement
RefinementMethod: DGSA-distance geometry simulated annealing, torsion angle dynamics
Software ordinal: 1
Details: 100 conformers, 30 conformers from 3/100 lowest energy DGSA refined conformers
NMR representativeSelection criteria: minimized average
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 30 / Conformers submitted total number: 16

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