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- PDB-1ksu: Crystal Structure of His505Tyr Mutant Flavocytochrome c3 from She... -

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Basic information

Entry
Database: PDB / ID: 1ksu
TitleCrystal Structure of His505Tyr Mutant Flavocytochrome c3 from Shewanella frigidimarina
Componentsflavocytochrome c
KeywordsOXIDOREDUCTASE / flavocytochrome c3 / fumarate reductase / H505Y
Function / homology
Function and homology information


fumarate reductase (quinol) / : / fumarate reductase (cytochrome) / anaerobic electron transport chain / anaerobic respiration / FMN binding / outer membrane-bounded periplasmic space / periplasmic space / electron transfer activity / 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 / Multiheme cytochrome c family profile. / Succinate dehydrogenase/fumarate reductase flavoprotein, catalytic domain superfamily ...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 / Multiheme cytochrome c family profile. / Succinate dehydrogenase/fumarate reductase flavoprotein, catalytic domain superfamily / 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 / FUMARIC ACID / PROTOPORPHYRIN IX CONTAINING FE / Fumarate reductase (cytochrome) / Fumarate reductase flavoprotein subunit
Similarity search - Component
Biological speciesShewanella frigidimarina (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsPankhurst, K.L. / Mowat, C.G. / Miles, C.S. / Leys, D. / Walkinshaw, M.D. / Reid, G.A. / Chapman, S.K.
CitationJournal: Biochemistry / Year: 2002
Title: Role of His505 in the soluble fumarate reductase from Shewanella frigidimarina.
Authors: Pankhurst, K.L. / Mowat, C.G. / Miles, C.S. / Leys, D. / Walkinshaw, M.D. / Reid, G.A. / Chapman, S.K.
History
DepositionJan 14, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 14, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 27, 2021Group: Data collection / Database references / Derived calculations
Category: database_2 / diffrn_source ...database_2 / diffrn_source / pdbx_struct_conn_angle / struct_conn / 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_asym_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_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_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_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_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_atom_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_asym_id / _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_asym_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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Aug 16, 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: flavocytochrome c
B: flavocytochrome c
hetero molecules


Theoretical massNumber of molelcules
Total (without water)128,08616
Polymers121,3052
Non-polymers6,78114
Water33,6341867
1
A: flavocytochrome c
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,0438
Polymers60,6521
Non-polymers3,3917
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: flavocytochrome c
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,0438
Polymers60,6521
Non-polymers3,3917
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)76.989, 87.274, 89.366
Angle α, β, γ (deg.)90.00, 104.43, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein flavocytochrome c / FLAVOCYTOCHROME C3 / FUMARATE REDUCTASE FLAVOPROTEIN SUBUNIT


Mass: 60652.273 Da / Num. of mol.: 2 / Mutation: H505Y
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, EC: 1.3.99.1

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Non-polymers , 5 types, 1881 molecules

#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#3: Chemical
ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


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


Mass: 785.550 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#5: Chemical ChemComp-FUM / FUMARIC ACID


Mass: 116.072 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H4O4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1867 / 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: 2.4 Å3/Da / Density % sol: 48.67 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: PEG8000, TrisHCl, NaCl, sodium fumarate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 8.5
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
1100 mMTris-HCl1reservoirpH7.4-8.2
280 mM1reservoirNaCl
316-19 %PEG80001reservoir
410 mMfumarate1reservoir
56 mg/mlprotein1drop
610 mMTris-HCl1droppH8.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7B / Wavelength: 0.8459 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Sep 7, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8459 Å / Relative weight: 1
ReflectionResolution: 2→20 Å / Num. all: 536347 / Num. obs: 77608 / % possible obs: 99.2 % / Observed criterion σ(I): 0 / Redundancy: 6.9 % / Biso Wilson estimate: 16 Å2 / Rmerge(I) obs: 0.072 / Net I/σ(I): 11.3
Reflection shellResolution: 2→2.07 Å / Rmerge(I) obs: 0.223 / Mean I/σ(I) obs: 3.32 / Num. unique all: 7631 / % possible all: 97.9
Reflection
*PLUS
Num. measured all: 536347 / Rmerge(I) obs: 0.072
Reflection shell
*PLUS
Rmerge(I) obs: 0.223

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Processing

Software
NameClassification
AMoREphasing
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1QJD

1qjd


Resolution: 2→15 Å / SU B: 3.9701 / SU ML: 0.11326 / Cross valid method: FREE R / σ(F): 0 / ESU R: 0.19912 / ESU R Free: 0.18659 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2386 3852 5 %random
Rwork0.167 ---
all0.167 76776 --
obs-72924 --
Displacement parametersBiso mean: 16 Å2
Refinement stepCycle: LAST / Resolution: 2→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8418 0 468 1867 10753
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_angle_d2.2
X-RAY DIFFRACTIONp_bond_d0.012
LS refinement shellResolution: 2→2.091 Å
RfactorNum. reflection
Rfree0.221 484
Rwork0.154 -
obs-8938
Refinement
*PLUS
Highest resolution: 2 Å / Lowest resolution: 20 Å / % reflection Rfree: 5 % / Rfactor all: 0.167 / Rfactor Rfree: 0.2386 / Rfactor Rwork: 0.167
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_angle_d
X-RAY DIFFRACTIONp_angle_deg2.4
LS refinement shell
*PLUS
Rfactor Rfree: 0.221 / Rfactor Rwork: 0.154

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