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- PDB-1qq3: THE SOLUTION STRUCTURE OF THE HEME BINDING VARIANT ARG98CYS OF OX... -

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Basic information

Entry
Database: PDB / ID: 1qq3
TitleTHE SOLUTION STRUCTURE OF THE HEME BINDING VARIANT ARG98CYS OF OXIDIZED ESCHERICHIA COLI CYTOCHROME B562
ComponentsCYTOCHROME B562
KeywordsELECTRON TRANSPORT / FOUR HELIX BUNDLE / HEMOPROTEIN
Function / homology
Function and homology information


electron transport chain / periplasmic space / electron transfer activity / iron ion binding / heme binding
Similarity search - Function
Cytochrome c/b562 / Cytochrome b562 / Cytochrome b562 / Cytochrome c/b562 / Four Helix Bundle (Hemerythrin (Met), subunit A) / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
HEME B/C / Soluble cytochrome b562
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodSOLUTION NMR / TORSION ANGLE DYNAMICS, ENERGY MINIMIZATION
Model type detailsminimized average
AuthorsArnesano, F. / Banci, L. / Bertini, I. / Ciofi-Baffoni, S. / Barker, P.D. / Woodyear, T.
CitationJournal: Biochemistry / Year: 2000
Title: Structural consequences of b- to c-type heme conversion in oxidized Escherichia coli cytochrome b562.
Authors: Arnesano, F. / Banci, L. / Bertini, I. / Ciofi-Baffoni, S. / Woodyear, T.L. / Johnson, C.M. / Barker, P.D.
History
DepositionJun 10, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 24, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 3, 2021Group: 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_conn_angle / pdbx_struct_oper_list / struct_conn / 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_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.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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 9, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature / pdbx_validate_chiral

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CYTOCHROME B562
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,3642
Polymers11,7451
Non-polymers6191
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)1 / -ENERGY MINIMIZED AVERAGE STRUCTURE
Representativeminimized average structure

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Components

#1: Protein CYTOCHROME B562


Mass: 11745.190 Da / Num. of mol.: 1 / Mutation: R98C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Plasmid: PCEB562 / Production host: Escherichia coli (E. coli) / References: UniProt: P0ABE7
#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
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D NOESY
2223D 15N-SEPARATED NOESY
232HNHA
1411D NOE

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Sample preparation

Details
Solution-IDContents
13MM R98C CYTOCHROME B562; 500MM PHOSPHATE BUFFER; 90% H2O, 10% D2O
22.5MM R98C CYTOCHROME B562; 500MM PHOSPHATE BUFFER; 90% H2O, 10% D2O
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
1500mM PHOSPHATE 4.8AMBIENT 298 K
2500mM PHOSPHATE 4.8AMBIENT 298 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCEBrukerAVANCE8001
Bruker AVANCEBrukerAVANCE6002

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMRprocessing
DYANA1.5GUENTERT P., MUMENTHALER, C., & WUTHRICH, K.structure solution
XEASYECCLES, C., GUENTERT P., BILLETER, M., & WUTHRICH, K.data analysis
PSEUDODYANABANCI, L., BERTINI, I., CREMONINI, M.A., GORI SAVELLINI, G., LUCHINAT, C., WUTHRICH, K. & GUENTERT, P.structure solution
Amber5PEARLMAN, D.A., CASE, D.A., CALDWELL, J.W., ROSS, W.S., CHEATHAM, T.E., FERGUSON, D.M., SEIBEL, G.L., SINGH, U.C., WEINER, P.K., & KOLLMAN, P.A.refinement
RefinementMethod: TORSION ANGLE DYNAMICS, ENERGY MINIMIZATION / Software ordinal: 1
Details: A TOTAL OF 4325 NOESY CROSS-PEAKS WAS ASSIGNED, INTEGRATED AND TRANSFORMED IN UPPER DISTANCE LIMITS; 23 DISTANCE CONSTRAINTS WERE DERIVED FROM 1D NOE EXPERIMENTS INVOLVING FAST RELAXING ...Details: A TOTAL OF 4325 NOESY CROSS-PEAKS WAS ASSIGNED, INTEGRATED AND TRANSFORMED IN UPPER DISTANCE LIMITS; 23 DISTANCE CONSTRAINTS WERE DERIVED FROM 1D NOE EXPERIMENTS INVOLVING FAST RELAXING PARAMAGNETIC SHIFTED SIGNALS. TOTALLY, THEY CORRESPONDED TO 2595 UPPER DISTANCE LIMITS, OF WHICH 2145 WERE FOUND TO BE MEANINGFUL. IN ADDITION, 45 3JHNHA COUPLINGS OBTAINED FROM THE HNHA 3D SPECTRUM AND 397 PCS WERE USED FOR THE STRUCTURE CALCULATIONS.
NMR representativeSelection criteria: minimized average structure
NMR ensembleConformer selection criteria: ENERGY MINIMIZED AVERAGE STRUCTURE
Conformers submitted total number: 1

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