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- PDB-1q9i: The A251C:S430C double mutant of flavocytochrome c3 from Shewanel... -

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Basic information

Entry
Database: PDB / ID: 1q9i
TitleThe A251C:S430C double mutant of flavocytochrome c3 from Shewanella frigidimarina
Componentsflavocytochrome c3
KeywordsOXIDOREDUCTASE / flavocytochrome / fumarate reductase / disulfide
Function / homology
Function and homology information


fumarate reductase (quinol) / : / fumarate reductase (cytochrome) / FMN binding / periplasmic space / oxidoreductase activity / metal ion binding
Similarity search - Function
Tetrahaem cytochrome domain / Cytochrome c3 / Flavocytochrome c / : / Flavocytochrome C3; Chain A / Flavocytochrome C3; Chain A, domain 2 / Flavocytochrome C3; Chain A, domain 1 / Succinate dehydrogenase/fumarate reductase flavoprotein, catalytic domain / Succinate dehydrogenase/fumarate reductase flavoprotein, catalytic domain superfamily / Multiheme cytochrome c family profile. ...Tetrahaem cytochrome domain / Cytochrome c3 / Flavocytochrome c / : / Flavocytochrome C3; Chain A / Flavocytochrome C3; Chain A, domain 2 / Flavocytochrome C3; Chain A, domain 1 / Succinate dehydrogenase/fumarate reductase flavoprotein, catalytic domain / Succinate dehydrogenase/fumarate reductase flavoprotein, catalytic domain superfamily / Multiheme cytochrome c family profile. / FAD-dependent oxidoreductase 2, FAD binding domain / FAD binding domain / Multiheme cytochrome superfamily / FAD/NAD(P)-binding domain / FAD/NAD(P)-binding domain / Zinc finger C2H2-type / 3-Layer(bba) Sandwich / FAD/NAD(P)-binding domain superfamily / Alpha-Beta Complex / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / HEME C / MALATE LIKE INTERMEDIATE / Fumarate reductase flavoprotein subunit / Fumarate reductase (cytochrome)
Similarity search - Component
Biological speciesShewanella frigidimarina (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsRothery, E.L. / Mowat, C.G. / Miles, C.S. / Walkinshaw, M.D. / Reid, G.A. / Chapman, S.K.
CitationJournal: Biochemistry / Year: 2004
Title: Probing Domain Mobility in a Flavocytochrome
Authors: Rothery, E.L. / Mowat, C.G. / Miles, C.S. / Mott, S. / Walkinshaw, M.D. / Reid, G.A. / Chapman, S.K.
History
DepositionAug 25, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 4, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 14, 2016Group: Other
Revision 2.0Mar 3, 2021Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_distant_solvent_atoms / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_conn_angle / pdbx_validate_close_contact / struct_conn / struct_conn_type / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.name / _chem_comp.pdbx_synonyms / _entity.formula_weight / _entity.pdbx_description / _pdbx_entity_nonpoly.comp_id / _pdbx_entity_nonpoly.name / _pdbx_nonpoly_scheme.mon_id / _pdbx_nonpoly_scheme.pdb_mon_id / _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_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_comp_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_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _pdbx_validate_close_contact.auth_comp_id_2 / _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_site.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id / _struct_site_gen.auth_comp_id / _struct_site_gen.label_comp_id
Revision 2.1Oct 27, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 2.2Aug 16, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 2.3Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: flavocytochrome c3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,0908
Polymers60,6751
Non-polymers3,4157
Water22,1221228
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)45.290, 91.885, 78.310
Angle α, β, γ (deg.)90.00, 91.50, 90.00
Int Tables number4
Cell settingmonoclinic
Space group name H-MP1211

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Components

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Protein , 1 types, 1 molecules A

#1: Protein flavocytochrome c3 / E.C.1.3.99.1 / fumarate reductase flavocytochrome precursor / Fumarate reductase flavoprotein subunit


Mass: 60675.375 Da / Num. of mol.: 1 / Fragment: flavoprotein subunit / Mutation: A251C,S430C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Shewanella frigidimarina (bacteria) / Gene: fcca / Plasmid: pMMB503 / Production host: Shewanella frigidimarina (bacteria) / Strain (production host): EG301
References: UniProt: Q02469, UniProt: Q07WU7*PLUS, EC: 1.3.99.1

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Non-polymers , 5 types, 1235 molecules

#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#3: Chemical
ChemComp-HEC / HEME C


Mass: 618.503 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C34H34FeN4O4
#4: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#5: Chemical ChemComp-TEO / MALATE LIKE INTERMEDIATE


Mass: 132.072 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H4O5
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1228 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.68 Å3/Da / Density % sol: 54.18 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8
Details: PEG 8000, TrisHCl, NaCl, fumarate, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX14.2 / Wavelength: 0.975 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: May 22, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.975 Å / Relative weight: 1
ReflectionResolution: 1.6→24 Å / Num. all: 84374 / Num. obs: 77814 / % possible obs: 92.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 20.607 Å2 / Rmerge(I) obs: 0.058 / Net I/σ(I): 14.31
Reflection shellResolution: 1.6→1.66 Å / Rmerge(I) obs: 0.345 / Mean I/σ(I) obs: 2.34 / Num. unique all: 8004 / % possible all: 95.5

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Processing

Software
NameVersionClassification
DENZOdata reduction
TRUNCATEdata reduction
AMoREphasing
REFMAC5.1.24refinement
CCP4(TRUNCATE)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb id 1qjd

1qjd


Resolution: 1.6→24 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.951 / SU B: 1.533 / SU ML: 0.054 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.086 / ESU R Free: 0.091 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.19711 3884 5 %RANDOM
Rwork0.15526 ---
obs0.15733 73913 92.24 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 20.607 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å2-0.62 Å2
2--0.06 Å20 Å2
3----0.09 Å2
Refinement stepCycle: LAST / Resolution: 1.6→24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4190 0 235 1228 5653
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0214527
X-RAY DIFFRACTIONr_angle_refined_deg1.4892.0826193
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0395567
X-RAY DIFFRACTIONr_chiral_restr0.1110.2671
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.023432
X-RAY DIFFRACTIONr_nbd_refined0.250.22418
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1360.2900
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2660.224
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3120.231
X-RAY DIFFRACTIONr_mcbond_it0.7691.52795
X-RAY DIFFRACTIONr_mcangle_it1.29224450
X-RAY DIFFRACTIONr_scbond_it2.23231732
X-RAY DIFFRACTIONr_scangle_it3.4034.51743
LS refinement shellResolution: 1.6→1.641 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.235 272
Rwork0.232 5622

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