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- PDB-1qjd: Flavocytochrome C3 from Shewanella frigidimarina -

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Basic information

Entry
Database: PDB / ID: 1qjd
TitleFlavocytochrome C3 from Shewanella frigidimarina
ComponentsFLAVOCYTOCHROME C3
KeywordsOXIDOREDUCTASE / FUMARATE REDUCTASE / RESPIRATORY FUMARATE REDUCTASE
Function / homology
Function and homology information


fumarate reductase (quinol) / : / succinate dehydrogenase / 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 / 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 / HEME C / MALATE LIKE INTERMEDIATE / Fumarate reductase flavoprotein subunit / Fumarate reductase flavoprotein subunit
Similarity search - Component
Biological speciesSHEWANELLA FRIGIDIMARINA (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.8 Å
AuthorsTaylor, P. / Pealing, S.L. / Reid, G.A. / Chapman, S.K. / Walkinshaw, M.D.
CitationJournal: Nat.Struct.Biol. / Year: 1999
Title: Structural and Mechanistic Mapping of a Unique Fumarate Reductase
Authors: Taylor, P. / Pealing, S.L. / Reid, G.A. / Chapman, S.K. / Walkinshaw, M.D.
History
DepositionJun 23, 1999Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 21, 1999Provider: repository / Type: Initial release
Revision 1.1Mar 18, 2015Group: Data collection / Derived calculations ...Data collection / Derived calculations / Non-polymer description / Other / Refinement description / 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

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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)64,1349
Polymers60,6271
Non-polymers3,5078
Water10,377576
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)45.393, 91.946, 78.288
Angle α, β, γ (deg.)90.00, 91.09, 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 FLAVOCYTOCHROME C3


Mass: 60627.242 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SHEWANELLA FRIGIDIMARINA (bacteria) / Strain: NCIMB400 / References: UniProt: Q02469, UniProt: Q07WU7*PLUS

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Non-polymers , 6 types, 584 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-TEO / MALATE LIKE INTERMEDIATE


Mass: 132.072 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H4O5
#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.: 576 / 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: 2.32 Å3/Da / Density % sol: 47 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 8.4
Details: HANGING DROP, 50-100MM TRISHCL PH 7.4 80MM NACL 17-20% PEG 8000 10MM FUM
Crystal
*PLUS
Crystal grow
*PLUS
Temperature: 4 ℃ / Method: vapor diffusion, hanging drop / Details: Pealing, S.L., (1999) J. Struct. Biol., 127, 76.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
150-100 mMTris-HCl1reservoir
280 mM1reservoirNaCl
317-20 %PEG80001reservoir
4+-10 mMfumarate1reservoir
56-10 mg/mlprotain1drop
610 mMTris-HCl1drop

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX7.2 / Wavelength: 1.488, 1.736, 1.738
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Aug 20, 1996
RadiationMonochromator: GE(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.4881
21.7361
31.7381
ReflectionResolution: 1.8→24 Å / Num. obs: 54988 / % possible obs: 92.5 % / Redundancy: 7.2 % / Rmerge(I) obs: 0.083 / Net I/σ(I): 13.2
Reflection shellResolution: 1.8→1.83 Å / Redundancy: 3.46 % / Rmerge(I) obs: 0.207 / Mean I/σ(I) obs: 6.29 / % possible all: 94

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
SHELXL-97phasing
SOLVEphasing
SHELXL-97refinement
RefinementMethod to determine structure: MAD / Resolution: 1.8→24 Å / Num. parameters: 20171 / Num. restraintsaints: 18190 / Cross valid method: FREE R-VALUE / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER
Details: SER 113 HAS ONLY PARTIAL DENSITY AND THIS IS RESPONSIBLE FOR THE POOR QUALITY OF GLU A 114. RESIDUE ARG A 487 SHOWS POOR DENSITY FOR ATOMS CG AND CD. DATA WAS COLLECTED AT WAVELENGTHS 1.736 ...Details: SER 113 HAS ONLY PARTIAL DENSITY AND THIS IS RESPONSIBLE FOR THE POOR QUALITY OF GLU A 114. RESIDUE ARG A 487 SHOWS POOR DENSITY FOR ATOMS CG AND CD. DATA WAS COLLECTED AT WAVELENGTHS 1.736 AND 1.739 ANGSTROM USING THE EMBL/DESY, HAMBURG BEAMLINE X31 SYNCHROTRON. THE SRS DATA AT WAVELENGTH 1.488 ANGSTROM WAS USED IN THE REFINEMENT.
RfactorNum. reflection% reflectionSelection details
Rfree0.2666 5513 11.2 %RANDOM
all0.1921 49415 --
obs0.1921 -83.1 %-
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: 5042
Refinement stepCycle: LAST / Resolution: 1.8→24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4217 0 241 576 5034
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_planes0.0261
X-RAY DIFFRACTIONs_zero_chiral_vol0.033
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.042
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.009
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.068
X-RAY DIFFRACTIONs_approx_iso_adps0
Software
*PLUS
Name: SHELXL-97 / Classification: refinement
Refinement
*PLUS
Rfactor Rwork: 0.1921
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: s_plane_restr / Dev ideal: 0.0261

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