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- PDB-1e39: Flavocytochrome C3 from Shewanella frigidimarina histidine 365 mu... -

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Basic information

Entry
Database: PDB / ID: 1.0E+39
TitleFlavocytochrome C3 from Shewanella frigidimarina histidine 365 mutated to alanine
ComponentsFUMARATE REDUCTASE FLAVOPROTEIN SUBUNIT
KeywordsOXIDOREDUCTASE / FUMARATE REDUCTASE MUTANT H365A / RESPIRATORY FUMARATE REDUCTASE
Function / homology
Function and homology information


anaerobic electron transport chain / succinate dehydrogenase / anaerobic respiration / FMN binding / outer membrane-bounded periplasmic space / electron transfer activity / 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 / 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 / HEME C / Fumarate reductase flavoprotein subunit / Fumarate reductase flavoprotein subunit
Similarity search - Component
Biological speciesSHEWANELLA FRIGIDIMARINA (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsDoherty, M.K. / Pealing, S.L. / Miles, C.S. / Moysey, R. / Taylor, P. / Walkinshaw, M.D. / Reid, G.A. / Chapman, S.K.
CitationJournal: Biochemistry / Year: 2000
Title: Identification of the Active Site Acid/Base Catalyst in a Bacterial Fumarate Reductase: A Kinetic and Crystallographic Study
Authors: Doherty, M.K. / Pealing, S.L. / Miles, C.S. / Moysey, R. / Taylor, P. / Walkinshaw, M.D. / Reid, G.A. / Chapman, S.K.
History
DepositionJun 7, 2000Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 18, 2000Provider: repository / Type: Initial release
Revision 1.1Aug 24, 2011Group: Database references / Derived calculations ...Database references / Derived calculations / Non-polymer description / Other / Structure summary / Version format compliance
Revision 1.2May 8, 2019Group: Data collection / Derived calculations ...Data collection / Derived calculations / Experimental preparation / Other
Category: database_PDB_rev / database_PDB_rev_record ...database_PDB_rev / database_PDB_rev_record / exptl_crystal_grow / pdbx_database_proc / pdbx_database_status / struct_conn
Item: _exptl_crystal_grow.method / _pdbx_database_status.recvd_author_approval / _struct_conn.pdbx_leaving_atom_flag
Revision 1.3May 22, 2019Group: Data collection / Refinement description / Category: refine / Item: _refine.pdbx_ls_cross_valid_method
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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.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 2.1Dec 6, 2023Group: Refinement description / Category: pdbx_initial_refinement_model

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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)64,0519
Polymers60,5601
Non-polymers3,4918
Water10,899605
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)45.571, 92.172, 78.489
Angle α, β, γ (deg.)90.00, 91.08, 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 C / FLAVOCYTOCHROME C3 / FCC3


Mass: 60560.172 Da / Num. of mol.: 1 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SHEWANELLA FRIGIDIMARINA (bacteria) / Strain: NCIMB400 / Production host: SHEWANELLA FRIGIDIMARINA (bacteria)
References: UniProt: Q07WU7, UniProt: P0C278*PLUS, succinate dehydrogenase

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Non-polymers , 6 types, 613 molecules

#2: Chemical
ChemComp-HEC / HEME C / Heme C


Mass: 618.503 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C34H34FeN4O4
#3: 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
#4: Chemical ChemComp-FUM / FUMARIC ACID / Fumaric acid


Mass: 116.072 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H4O4
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 605 / Source method: isolated from a natural source / Formula: H2O

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Details

Compound detailsCHAIN A ENGINEERED MUTATION HIS365ALA

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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: 2.24 Å3/Da / Density % sol: 54.8 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 8.4
Details: HANGING DROP, 50-100MM TRIS-HCL PH 7.4, 80MM NACL, 17-20% PEG 8000, 10MM FUMARATE
Crystal grow
*PLUS
Temperature: 4 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
1100 mMTris-HCl1reservoir
280 mM1reservoirNaCl
317-20 %PEG80001reservoir
410 mMfumarate1reservoir
56 mg/mlprotain1drop
610 mMTris-HCl1drop

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX9.6 / Wavelength: 0.87
DetectorType: ADSC CCD / Detector: CCD / Date: Oct 9, 1999 / Details: RH COATED SI MIRROR
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.87 Å / Relative weight: 1
ReflectionResolution: 1.8→18 Å / Num. obs: 54314 / % possible obs: 90.7 % / Redundancy: 2.699 % / Rmerge(I) obs: 0.049 / Net I/σ(I): 19.01
Reflection shellResolution: 1.8→1.83 Å / Redundancy: 1.97 % / Rmerge(I) obs: 0.117 / Mean I/σ(I) obs: 7.14 / % possible all: 74.9
Reflection
*PLUS
Lowest resolution: 24 Å / Num. measured all: 265858
Reflection shell
*PLUS
Highest resolution: 1.8 Å

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Processing

Software
NameClassification
SHELXL-97refinement
DENZOdata reduction
SCALEPACKdata scaling
SHELXL-97phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1QJD

1qjd


Resolution: 1.8→18 Å / Num. parameters: 20251 / Num. restraintsaints: 18150 / Cross valid method: FREE R-VALUE / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.247 5513 10.7 %RANDOM
all0.1814 51592 --
obs0.1814 -86 %-
Solvent computationSolvent model: MOEWS & KRETSINGER, J.MOL.BIOL.91(1973)201-2
Refine analyzeNum. disordered residues: 0 / Occupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 5062
Refinement stepCycle: LAST / Resolution: 1.8→18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4212 0 240 605 5057
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.007
X-RAY DIFFRACTIONs_angle_d0.022
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.0257
X-RAY DIFFRACTIONs_zero_chiral_vol0.034
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.043
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.007
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.069
X-RAY DIFFRACTIONs_approx_iso_adps0
Software
*PLUS
Name: SHELXL-97 / Classification: refinement
Refinement
*PLUS
Rfactor Rfree: 0.247 / Rfactor Rwork: 0.1814
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_plane_restr0.0257
X-RAY DIFFRACTIONs_chiral_restr0.034

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