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- PDB-1k0t: NMR SOLUTION STRUCTURE OF UNBOUND, OXIDIZED PHOTOSYSTEM I SUBUNIT... -

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Basic information

Entry
Database: PDB / ID: 1k0t
TitleNMR SOLUTION STRUCTURE OF UNBOUND, OXIDIZED PHOTOSYSTEM I SUBUNIT PSAC, CONTAINING [4FE-4S] CLUSTERS FA AND FB
ComponentsPSAC SUBUNIT OF PHOTOSYSTEM I
KeywordsELECTRON TRANSPORT / IRON-SULFUR PROTEIN / SOLUTION STRUCTURE / PARAMAGNETIC / CONFORMATIONAL CHANGE / PHOTOSYSTEM I / PSAC
Function / homology
Function and homology information


thylakoid membrane / photosystem I / photosystem I / photosynthetic electron transport in photosystem I / 4 iron, 4 sulfur cluster binding / electron transfer activity / metal ion binding
Similarity search - Function
Alpha-Beta Plaits - #20 / Photosystem I protein PsaC / 4Fe-4S dicluster domain / 4Fe-4S ferredoxin, iron-sulphur binding, conserved site / 4Fe-4S ferredoxin-type iron-sulfur binding region signature. / 4Fe-4S ferredoxin-type iron-sulfur binding domain profile. / 4Fe-4S ferredoxin-type, iron-sulphur binding domain / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
IRON/SULFUR CLUSTER / Photosystem I iron-sulfur center
Similarity search - Component
Biological speciesSynechococcus sp. (bacteria)
MethodSOLUTION NMR / torsion angle dynamics, a simulated annealing algorithm
AuthorsAntonkine, M.L. / Liu, G. / Bentrop, D. / Bryant, D.A. / Bertini, I. / Luchinat, C. / Golbeck, J.H. / Stehlik, D.
CitationJournal: J.Biol.Inorg.Chem. / Year: 2002
Title: Solution structure of the unbound, oxidized Photosystem I subunit PsaC, containing [4Fe-4S] clusters F(A) and F(B): a conformational change occurs upon binding to photosystem I.
Authors: Antonkine, M.L. / Liu, G. / Bentrop, D. / Bryant, D.A. / Bertini, I. / Luchinat, C. / Golbeck, J.H. / Stehlik, D.
History
DepositionSep 20, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 5, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3May 1, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
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Assembly

Deposited unit
A: PSAC SUBUNIT OF PHOTOSYSTEM I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,3953
Polymers8,6921
Non-polymers7032
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)30 / 400LEAST RESTRAINT VIOLATIONS
Representative

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Components

#1: Protein PSAC SUBUNIT OF PHOTOSYSTEM I


Mass: 8692.039 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Synechococcus sp. (bacteria) / Strain: PCC 7002 / Gene: psac / Plasmid: pet-3d / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 DE3 / References: UniProt: P31087
#2: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe4S4

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D NOESY
1212D DQF-COSY
1312D TOCSY
1411D-NOE
1513D HSQC-NOESY
1613D-HSQC-TOCSY
1711H-15N HSQC
181HNHA
391TOCSY
31012D NOESY
NMR detailsText: THE STRUCTURE WAS DETERMINED USING 1H AND 15N NMR SPECTROSCOPY. EXPERIMENTAL DETAILS CAN BE FOUND IN THE JRNL CITATION ABOVE.

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Sample preparation

Details
Solution-IDContentsSolvent system
12.5mM PsaC U-15N; 25mM phosphate buffer pH=7.6; 90% H2O, 10% D2O90% H2O/10% D2O
22.5mM PsaC U-15N; 25mM phosphate buffer pH=8.0; 90% H2O, 10% D2O90% H2O/10% D2O
32.5mM PsaC; 25mM phosphate buffer pH=8.0; 99% D2O99% D2O
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
125 mM 7.60 1 atm285.00 K
225 mM 8.0 1 atm285.00 K
325 mM 7.6 1 atm298.00 K
425 mM 8.0 1 atm298.00 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCE 800BrukerAVANCE 8008001
Bruker AVANCE 600BrukerAVANCE 6006002
Bruker DRX 500BrukerDRX 5005003

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Processing

NMR software
NameVersionDeveloperClassification
DYANA1.5Guentert P, Mumenthaler C., Wuethrich K.structure solution
DYANA1.5Guentert P, Mumenthaler C., Wuethrich K.refinement
RefinementMethod: torsion angle dynamics, a simulated annealing algorithm
Software ordinal: 1
NMR ensembleConformer selection criteria: LEAST RESTRAINT VIOLATIONS / Conformers calculated total number: 400 / Conformers submitted total number: 30

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