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- PDB-2kmf: Solution Structure of Psb27 from cyanobacterial photosystem II -

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Basic information

Entry
Database: PDB / ID: 2kmf
TitleSolution Structure of Psb27 from cyanobacterial photosystem II
ComponentsPhotosystem II 11 kDa protein
KeywordsPHOTOSYNTHESIS / Psb27 / photosystem II / helical bundle / cyanobacteria
Function / homology
Function and homology information


plasma membrane-derived thylakoid photosystem II / photosystem II repair / thylakoid lumen / photosystem II assembly / plasma membrane-derived thylakoid membrane
Similarity search - Function
Photosystem II Pbs27 / Photosystem II Psb27, cyanobacteria / Photosystem II Pbs27 / Photosystem II Pbs27 superfamily / Photosystem II Pbs27 / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Prokaryotic membrane lipoprotein lipid attachment site profile. / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Photosystem II lipoprotein Psb27
Similarity search - Component
Biological speciesSynechocystis sp. (bacteria)
MethodSOLUTION NMR / DGSA-distance geometry simulated annealing
Model detailsclosest to the average, model 1
AuthorsMabbitt, P.D. / Rautureau, G.J.P. / Day, C.L. / Wilbanks, S.M. / Eaton-Rye, J.J. / Hinds, M.G.
CitationJournal: Biochemistry / Year: 2009
Title: Solution structure of Psb27 from cyanobacterial photosystem II
Authors: Mabbitt, P.D. / Rautureau, G.J. / Day, C.L. / Wilbanks, S.M. / Eaton-Rye, J.J. / Hinds, M.G.
History
DepositionJul 28, 2009Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Sep 8, 2009Provider: 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_software ...database_2 / pdbx_nmr_software / 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_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: Photosystem II 11 kDa protein


Theoretical massNumber of molelcules
Total (without water)12,6451
Polymers12,6451
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 / 256structures with the least restraint violations
RepresentativeModel #1closest to the average

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Components

#1: Protein Photosystem II 11 kDa protein /


Mass: 12645.056 Da / Num. of mol.: 1 / Fragment: UNP residues 25-134
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Synechocystis sp. (bacteria) / Strain: PCC 6803 / Gene: psb27 / Plasmid: pGEX-6P-3 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / Variant (production host): DE3 / References: UniProt: P74367

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR / Details: Solution structure of Psb27
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-1H NOESY
1222D 1H-15N HSQC
1332D 1H-13C HSQC
1433D HNCA
1533D HN(CA)CB
1633D HNCO
1733D HCACO
1833D (H)CCH-TOCSY
1933D 1H-15N NOESY
11033D 1H-13C NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
10.5mM Psb27-1, 5% D2O-2, 95% H2O-3, 20mM sodium phosphate-4, 50mM sodium chloride-5, 5mM TCEP-6, 1mM sodium azide-7, 95% H2O/5% D2O95% H2O/5% D2O
20.5mM [U-100% 15N] Psb27-8, 5% D2O-9, 95% H2O-10, 20mM sodium phosphate-11, 50mM sodium chloride-12, 5mM TCEP-13, 1mM sodium azide-14, 95% H2O/5% D2O95% H2O/5% D2O
30.5mM [U-100% 13C; U-100% 15N] Psb27-15, 5% D2O-16, 95% H2O-17, 20mM sodium phosphate-18, 50mM sodium chloride-19, 5mM TCEP-20, 1mM sodium azide-21, 95% H2O/5% D2O95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.5 mMPsb27-11
5 mMD2O-21
95 mMH2O-31
20 mMsodium phosphate-41
50 mMsodium chloride-51
5 mMTCEP-61
1 mMsodium azide-71
0.5 mMPsb27-8[U-100% 15N]2
5 mMD2O-92
95 mMH2O-102
20 mMsodium phosphate-112
50 mMsodium chloride-122
5 mMTCEP-132
1 mMsodium azide-142
0.5 mMPsb27-15[U-100% 13C; U-100% 15N]3
5 mMD2O-163
95 mMH2O-173
20 mMsodium phosphate-183
50 mMsodium chloride-193
5 mMTCEP-203
1 mMsodium azide-213
Sample conditionsIonic strength: 100 / pH: 6.70 / Pressure: ambient / Temperature: 298.15 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE5001
Bruker AvanceBrukerAVANCE8002

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Processing

NMR software
NameVersionDeveloperClassification
TopSpin2.1Bruker Biospincollection
TopSpin2.1Bruker Biospinprocessing
XEASY3.13Bartels et al.data analysis
CYANA2.1Guntert, Mumenthaler, Wuthrichstructure solution
X-PLOR NIH2.22Schwieters, Kuszewski, Tjandra, Clorerefinement
RefinementMethod: DGSA-distance geometry simulated annealing / Software ordinal: 1
NMR constraintsNOE constraints total: 2802 / NOE intraresidue total count: 516 / NOE long range total count: 771 / NOE medium range total count: 909 / NOE sequential total count: 606 / Hydrogen bond constraints total count: 57
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 256 / Conformers submitted total number: 20 / Maximum upper distance constraint violation: 0.3 Å / Representative conformer: 1
NMR ensemble rmsDistance rms dev: 0.0018 Å / Distance rms dev error: 0.0001 Å

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