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- PDB-1qo8: The structure of the open conformation of a flavocytochrome c3 fu... -

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Basic information

Entry
Database: PDB / ID: 1qo8
TitleThe structure of the open conformation of a flavocytochrome c3 fumarate reductase
ComponentsFLAVOCYTOCHROME C3 FUMARATE REDUCTASE
KeywordsOXIDOREDUCTASE
Function / homology
Function and homology information


Oxidoreductases; Acting on the CH-CH group of donors; With a cytochrome as acceptor / steroid metabolic process / 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 / 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 / PROTOPORPHYRIN IX CONTAINING FE / Probable fumarate reductase Ifc3
Similarity search - Component
Biological speciesSHEWANELLA FRIGIDIMARINA (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.15 Å
AuthorsBamford, V. / Dobbin, P.S. / Richardson, D.J. / Hemmings, A.M.
CitationJournal: Nat.Struct.Biol. / Year: 1999
Title: Open Conformation of a Flavocytochrome C3 Fumarate Reductase.
Authors: Bamford, V. / Dobbin, P.S. / Richardson, D.J. / Hemmings, A.M.
History
DepositionNov 4, 1999Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 2, 2000Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 24, 2019Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.4May 8, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_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_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: FLAVOCYTOCHROME C3 FUMARATE REDUCTASE
D: FLAVOCYTOCHROME C3 FUMARATE REDUCTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)128,03212
Polymers121,5292
Non-polymers6,50310
Water9,134507
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)71.770, 109.690, 227.320
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein FLAVOCYTOCHROME C3 FUMARATE REDUCTASE


Mass: 60764.484 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) SHEWANELLA FRIGIDIMARINA (bacteria) / Strain: NCIMB400 / References: UniProt: Q9Z4P0, succinate dehydrogenase
#2: Chemical
ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 507 / 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: 3.68 Å3/Da / Density % sol: 66.59 %
Crystal growpH: 6.5 / Details: pH 6.50
Crystal grow
*PLUS
pH: 7.5 / Method: vapor diffusion, hanging drop
Details: Bamford, V., (1999) Acta Crystallogr.,Sect., D55, 1222.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
110-15 mg/mlprotein1drop
250 mMsodium HEPES1drop
3100 mM1dropNaCl
46-15 %(w/v)PEG100001reservoir
5sodium MES1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7B / Wavelength: 0.8469, 1.033, 1.739, 1.741
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Apr 15, 1999
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.84691
21.0331
31.7391
41.7411
ReflectionResolution: 2.15→20 Å / Num. obs: 97968 / % possible obs: 91.4 % / Redundancy: 14.6 % / Rsym value: 0.038
Reflection shellResolution: 2.15→2.19 Å / Rsym value: 0.274 / % possible all: 91.4
Reflection
*PLUS
% possible obs: 93.4 % / Num. measured all: 1428311 / Rmerge(I) obs: 0.038
Reflection shell
*PLUS
% possible obs: 91.4 % / Rmerge(I) obs: 0.274

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Processing

Software
NameClassification
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MAD / Resolution: 2.15→20 Å / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.281 -5 %RANDOM
Rwork0.225 ---
obs-82429 93.4 %-
Refinement stepCycle: LAST / Resolution: 2.15→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8468 0 450 507 9425
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.015
X-RAY DIFFRACTIONp_angle_d0.013
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it
X-RAY DIFFRACTIONp_mcangle_it
X-RAY DIFFRACTIONp_scbond_it
X-RAY DIFFRACTIONp_scangle_it
X-RAY DIFFRACTIONp_plane_restr
X-RAY DIFFRACTIONp_chiral_restr
X-RAY DIFFRACTIONp_singtor_nbd
X-RAY DIFFRACTIONp_multtor_nbd
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor
X-RAY DIFFRACTIONp_staggered_tor
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor
Software
*PLUS
Name: REFMAC / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.225
Solvent computation
*PLUS
Displacement parameters
*PLUS
LS refinement shell
*PLUS
Rfactor Rfree: 0.295 / Rfactor obs: 0.258

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