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- PDB-2lzz: Solution structure of a mutant of the triheme cytochrome PpcA fro... -

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Basic information

Entry
Database: PDB / ID: 2lzz
TitleSolution structure of a mutant of the triheme cytochrome PpcA from Geobacter sulfurreducens sheds light on the role of the conserved aromatic residue F15
ComponentsCytochrome c, 3 heme-binding sites
KeywordsELECTRON TRANSPORT / Geobacter / Triheme cytochrome / Site-directed mutagenesis
Function / homologyCytochrome C3 / Cytochrome C3 / Alpha-Beta Complex / Alpha Beta / PROTOPORPHYRIN IX CONTAINING FE / :
Function and homology information
Biological speciesGeobacter sulfurreducens (bacteria)
MethodSOLUTION NMR / simulated annealing
AuthorsDantas, J.M. / Morgado, L. / Turner, D.L. / Salgueiro, C.A.
CitationJournal: Biochim.Biophys.Acta / Year: 2013
Title: Solution structure of a mutant of the triheme cytochrome PpcA from Geobacter sulfurreducens sheds light on the role of the conserved aromatic residue F15.
Authors: Dantas, J.M. / Morgado, L. / Pokkuluri, P.R. / Turner, D.L. / Salgueiro, C.A.
History
DepositionOct 12, 2012Deposition site: BMRB / Processing site: RCSB
Revision 1.0Jan 30, 2013Provider: repository / Type: Initial release
Revision 1.1Mar 13, 2013Group: Database references
Revision 1.2Oct 16, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_struct_conn_angle / struct_conn / struct_conn_type / struct_ref_seq_dif / 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_nmr_spectrometer.model / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_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_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_conn_type.id / _struct_ref_seq_dif.details / _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:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cytochrome c, 3 heme-binding sites
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,5644
Polymers7,7141
Non-polymers1,8493
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 200structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Cytochrome c, 3 heme-binding sites


Mass: 7714.133 Da / Num. of mol.: 1 / Mutation: F15L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Geobacter sulfurreducens (bacteria) / Strain: DL-1 / KN400 / Gene: GSU0612, KN400_0591, ppcA / Plasmid: pCK32 / Production host: Escherichia coli (E. coli) / References: UniProt: D7AFU0
#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C34H32FeN4O4
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
2122D 1H-15N HSQC
1212D 1H-1H TOCSY
1312D 1H-1H COSY
1412D 1H-1H NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
11 mM F15L polypeptide, 3 mM PROTOPORPHYRIN IX CONTAINING FE, 45 mM sodium phosphate, 0.04 % sodium azide, 93% H2O/7% D2O93% H2O/7% D2O
20.4 mM [U-100% 15N] F15L polypeptide, 3 mM PROTOPORPHYRIN IX CONTAINING FE, 45 mM sodium phosphate, 0.04 % sodium azide, 93% H2O/7% D2O93% H2O/7% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMF15L polypeptide-11
3 mMPROTOPORPHYRIN IX CONTAINING FE-21
45 mMsodium phosphate-31
0.04 %sodium azide-41
0.4 mMF15L polypeptide-5[U-100% 15N]2
3 mMPROTOPORPHYRIN IX CONTAINING FE-62
45 mMsodium phosphate-72
0.04 %sodium azide-82
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
11007.1ambient 298 K
2457.1ambient 298 K

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NMR measurement

NMR spectrometerType: Bruker Avance / Manufacturer: Bruker / Model: AVANCE / Field strength: 600 MHz

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Processing

NMR software
NameDeveloperClassification
TopSpinBruker Biospinprocessing
TopSpinBruker Biospincollection
SparkyGoddardchemical shift assignment
PARADYANATurner, D. L. Brennan, L. Chamberlin, S. G. Louro, R. O. Xavier, A. V.chemical shift calculation
PARADYANATurner, D. L. Brennan, L. Chamberlin, S. G. Louro, R. O. Xavier, A. V.refinement
MOLMOLKoradi, Billeter and Wuthrichsuperimposition
MOLMOLKoradi, Billeter and Wuthrichvisual inspection
CINGNabuurs, Spronk, Krieger, Maassen, Vriend and Vuistervalidation
RefinementMethod: simulated annealing / Software ordinal: 1
NMR constraintsNOE constraints total: 1822 / NOE intraresidue total count: 704 / NOE long range total count: 453 / NOE medium range total count: 300 / NOE sequential total count: 365
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 20 / Maximum lower distance constraint violation: 0.27 Å / Maximum upper distance constraint violation: 0.26 Å
NMR ensemble rmsDistance rms dev: 1.14 Å / Distance rms dev error: 0.1 Å

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