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- PDB-1b3i: NMR SOLUTION STRUCTURE OF PLASTOCYANIN FROM THE PHOTOSYNTHETIC PR... -

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Basic information

Entry
Database: PDB / ID: 1b3i
TitleNMR SOLUTION STRUCTURE OF PLASTOCYANIN FROM THE PHOTOSYNTHETIC PROKARYOTE, PROCHLOROTHRIX HOLLANDICA (MINIMIZED AVERAGE STRUCTURE)
ComponentsPROTEIN (PLASTOCYANIN)
KeywordsELECTRON TRANSPORT / TYPE I COPPER PROTEIN / PHOTOSYNTHESIS
Function / homology
Function and homology information


plasma membrane-derived thylakoid membrane / electron transfer activity / copper ion binding
Similarity search - Function
Plastocyanin, cyanobacteria / Plastocyanin / Blue (type 1) copper protein, plastocyanin-type / Blue (type 1) copper domain / Copper binding proteins, plastocyanin/azurin family / Blue (type 1) copper protein, binding site / Type-1 copper (blue) proteins signature. / Cupredoxins - blue copper proteins / Cupredoxin / Immunoglobulin-like ...Plastocyanin, cyanobacteria / Plastocyanin / Blue (type 1) copper protein, plastocyanin-type / Blue (type 1) copper domain / Copper binding proteins, plastocyanin/azurin family / Blue (type 1) copper protein, binding site / Type-1 copper (blue) proteins signature. / Cupredoxins - blue copper proteins / Cupredoxin / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
COPPER (I) ION / Plastocyanin
Similarity search - Component
Biological speciesProchlorothrix hollandica (bacteria)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsBabu, C.R. / Volkman, B.F. / Bullerjahn, G.S.
CitationJournal: Biochemistry / Year: 1999
Title: NMR solution structure of plastocyanin from the photosynthetic prokaryote, Prochlorothrix hollandica.
Authors: Babu, C.R. / Volkman, B.F. / Bullerjahn, G.S.
History
DepositionDec 11, 1998Deposition site: BNL / Processing site: RCSB
Revision 1.0Apr 27, 1999Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 16, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_conn_angle / pdbx_struct_oper_list / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_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.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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
Revision 1.4Dec 27, 2023Group: 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: PROTEIN (PLASTOCYANIN)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,2122
Polymers10,1491
Non-polymers641
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)1 / 40LOWEST TARGET FUNCTION
Representative

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Components

#1: Protein PROTEIN (PLASTOCYANIN) / PETE PROTEIN


Mass: 10148.560 Da / Num. of mol.: 1 / Mutation: T2S
Source method: isolated from a genetically manipulated source
Details: T2S MUTATION INTRODUCED TO CLONE IN EXPRESSION VECTOR
Source: (gene. exp.) Prochlorothrix hollandica (bacteria) / Description: INCLUSION BODIES WERE REFOLDED IN-VITRO / Cellular location: THYLAKOID LUMEN / Gene: PETE / Plasmid: PVAPC10
Cellular location (production host): CYTOPLASM - INCLUSION BODIES
Gene (production host): PETE / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)PLYSS / References: UniProt: P50057, EC: 1.10.99.1
#2: Chemical ChemComp-CU1 / COPPER (I) ION


Mass: 63.546 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cu
Sequence detailsT2S - INTRODUCED TO CLONE, R61A - MISTAKE IN GB ENTRY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111NOESY
121TOCSY
131DQF-COSY
NMR detailsText: MINIMIZED AVERAGE STRUCTURE. THE STRUCTURE WAS DETERMINED USING TWO- DIMENCIONAL NMR SPECTROSCOPY. WATER SUPPRESSION WAS ACHIEVED WITH A WATERGATE SEQ. WITH A 3-9-19 SELECTIVE INVERSION.

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Sample preparation

DetailsContents: 90% WATER/10% D2O
Sample conditionsIonic strength: 20mM POTASSIUM PHOSPHATE / pH: 7 / Pressure: 1 atm / Temperature: 298 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometerType: Bruker DMX750 / Manufacturer: Bruker / Model: DMX750 / Field strength: 750 MHz

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Processing

NMR software
NameVersionDeveloperClassification
DYANAP.GUNTERT, C.MUMENTHALER, K.WUTHRICHrefinement
DYANA1.5structure solution
Felixstructure solution
RefinementMethod: torsion angle dynamics / Software ordinal: 1
Details: REFINEMENT DETAILS ARE IN THE SUBMITTED FILE AND IN THE JRNL CITATION ABOVE. THE RESTRAINTS ARE IN THE FILES WITH THE 19 CONFORMERS.
NMR ensembleConformer selection criteria: LOWEST TARGET FUNCTION / Conformers calculated total number: 40 / Conformers submitted total number: 1

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