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- PDB-2b7r: Structure of E378D mutant flavocytochrome c3 -

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Basic information

Entry
Database: PDB / ID: 2b7r
TitleStructure of E378D mutant flavocytochrome c3
ComponentsFumarate reductase flavoprotein subunit
KeywordsOXIDOREDUCTASE / flavocytochrome c3 / fumarate reductase / proton delivery
Function / homology
Function and homology information


fumarate reductase (quinol) / anaerobic electron transport chain / : / succinate dehydrogenase / anaerobic respiration / FMN binding / outer membrane-bounded periplasmic space / electron transfer activity / periplasmic space / 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 / FAD-dependent oxidoreductase 2, FAD binding domain / FAD binding domain ...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 / FAD-dependent oxidoreductase 2, FAD binding domain / FAD binding domain / Multiheme cytochrome c family profile. / 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 / FUMARIC ACID / PROTOPORPHYRIN IX CONTAINING FE / Fumarate reductase flavoprotein subunit / Fumarate reductase flavoprotein subunit
Similarity search - Component
Biological speciesShewanella frigidimarina (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsPankhurst, K.L. / Mowat, C.G. / Rothery, E.L. / Miles, C.S. / Walkinshaw, M.D. / Reid, G.A. / Chapman, S.K.
CitationJournal: J.Biol.Chem. / Year: 2006
Title: A Proton Delivery Pathway in the Soluble Fumarate Reductase from Shewanella frigidimarina.
Authors: Pankhurst, K.L. / Mowat, C.G. / Rothery, E.L. / Hudson, J.M. / Jones, A.K. / Miles, C.S. / Walkinshaw, M.D. / Armstrong, F.A. / Reid, G.A. / Chapman, S.K.
History
DepositionOct 5, 2005Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 23, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 10, 2021Group: Data collection / Database references / Derived calculations
Category: database_2 / diffrn_source ...database_2 / diffrn_source / 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 / _diffrn_source.pdbx_synchrotron_site / _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_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_comp_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
Revision 1.4Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection / Category: atom_site / chem_comp_atom / chem_comp_bond
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_1 / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Fumarate reductase flavoprotein subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,0048
Polymers60,6131
Non-polymers3,3917
Water19,5281084
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)45.961, 92.879, 79.486
Angle α, β, γ (deg.)90.00, 91.17, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Fumarate reductase flavoprotein subunit / Flavocytochrome c3 / Flavocytochrome c / Fcc3


Mass: 60613.219 Da / Num. of mol.: 1 / Mutation: E378D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Shewanella frigidimarina (bacteria) / Gene: FCC / Plasmid: pMMB503EH / Production host: Shewanella frigidimarina (bacteria) / Strain (production host): EG301
References: UniProt: Q02469, UniProt: P0C278*PLUS, succinate dehydrogenase

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Non-polymers , 5 types, 1091 molecules

#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#3: Chemical
ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME / Heme B


Mass: 616.487 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#4: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE / Flavin adenine dinucleotide


Mass: 785.550 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#5: Chemical ChemComp-FUM / FUMARIC ACID / Fumaric acid


Mass: 116.072 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H4O4
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1084 / Source method: isolated from a natural source / Formula: H2O

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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: 2.61 Å3/Da / Density % sol: 52.6 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 0.1M TrisHCl, 80mM NaCl, 10mM Na fumarate, 15% PEG8000, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7B / Wavelength: 0.87 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Sep 9, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.87 Å / Relative weight: 1
ReflectionResolution: 1.7→20 Å / Num. all: 73408 / Num. obs: 72178 / % possible obs: 98.4 % / Biso Wilson estimate: 18.3 Å2 / Rmerge(I) obs: 0.067 / Net I/σ(I): 18.7
Reflection shellResolution: 1.7→1.76 Å / Rmerge(I) obs: 0.129 / Mean I/σ(I) obs: 6.9 / Num. unique all: 6862 / % possible all: 94.6

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Processing

Software
NameVersionClassification
REFMAC5.2.0003refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1QJD

1qjd


Resolution: 1.7→20 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.954 / SU B: 1.466 / SU ML: 0.05 / Cross valid method: THROUGHOUT / ESU R: 0.093 / ESU R Free: 0.089 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.18034 3629 5 %RANDOM
Rwork0.15646 ---
obs0.15768 68525 98.21 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 18.322 Å2
Baniso -1Baniso -2Baniso -3
1-0.71 Å20 Å2-0.16 Å2
2--0.4 Å20 Å2
3----1.12 Å2
Refinement stepCycle: LAST / Resolution: 1.7→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4176 0 234 1084 5494
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0214511
X-RAY DIFFRACTIONr_angle_refined_deg1.3142.0736171
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5795567
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.49125.029173
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.90215697
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.8731518
X-RAY DIFFRACTIONr_chiral_restr0.1110.2656
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.023438
X-RAY DIFFRACTIONr_nbd_refined0.2260.21796
X-RAY DIFFRACTIONr_nbtor_refined0.2830.22996
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1140.2577
X-RAY DIFFRACTIONr_metal_ion_refined0.0350.22
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1180.218
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1160.223
X-RAY DIFFRACTIONr_mcbond_it0.5611.52792
X-RAY DIFFRACTIONr_mcangle_it1.00924441
X-RAY DIFFRACTIONr_scbond_it1.77231851
X-RAY DIFFRACTIONr_scangle_it2.7424.51730
LS refinement shellResolution: 1.698→1.742 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.219 234 -
Rwork0.179 4638 -
obs--91.34 %

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