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- PDB-1jrz: Crystal structure of Arg402Tyr mutant flavocytochrome c3 from She... -

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Basic information

Entry
Database: PDB / ID: 1jrz
TitleCrystal structure of Arg402Tyr mutant flavocytochrome c3 from Shewanella frigidimarina
ComponentsFLAVOCYTOCHROME C
KeywordsOXIDOREDUCTASE / fumarate reductase / mutant / flavocytochrome
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 / oxidoreductase activity / electron transfer 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
AuthorsMowat, C.G. / Moysey, R. / Miles, C.S. / Leys, D. / Doherty, M.K. / Taylor, P. / Walkinshaw, M.D. / Reid, G.A. / Chapman, S.K.
CitationJournal: Biochemistry / Year: 2001
Title: Kinetic and crystallographic analysis of the key active site acid/base arginine in a soluble fumarate reductase.
Authors: Mowat, C.G. / Moysey, R. / Miles, C.S. / Leys, D. / Doherty, M.K. / Taylor, P. / Walkinshaw, M.D. / Reid, G.A. / Chapman, S.K.
History
DepositionAug 15, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 2, 2001Provider: 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: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / 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 / _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)128,04816
Polymers121,2662
Non-polymers6,78114
Water29,3641630
1
A: FLAVOCYTOCHROME C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,0248
Polymers60,6331
Non-polymers3,3917
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: FLAVOCYTOCHROME C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,0248
Polymers60,6331
Non-polymers3,3917
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)78.072, 87.906, 90.163
Angle α, β, γ (deg.)90.00, 105.03, 90.00
Int Tables number4
Cell settingmonoclinic
Space group name H-MP1211

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein FLAVOCYTOCHROME C / E.C.1.3.99.1 / FUMARATE REDUCTASE FLAVOPROTEIN SUBUNIT


Mass: 60633.219 Da / Num. of mol.: 2 / Mutation: R402Y
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Shewanella frigidimarina (bacteria) / Gene: fcc / Plasmid: pMMB503EH / Species (production host): Shewanella frigidimarina
Production host: Shewanella frigidimarina NCIMB 400 (bacteria)
Strain (production host): NCIMB400
References: UniProt: Q02469, UniProt: P0C278*PLUS, EC: 1.3.99.1

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Non-polymers , 5 types, 1644 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.: 1630 / 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: 2.46 Å3/Da / Density % sol: 50.07 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: PEG 8000, TrisHCl, sodium chloride, sodium fumarate, pH 7.5, VAPOR DIFFUSION, HANGING DROP at 277K
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 8.5
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
1100 mMTris-HCl1reservoir
280 mM1reservoirNaCl
316-19 %PEG80001reservoir
410 mMfumarate1reservoir
56 mg/mlprotein1drop
610 mMTris-HCl1drop

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 1.0332 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Apr 30, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 2→20 Å / Num. all: 79505 / Num. obs: 76643 / % possible obs: 96.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.073 / Net I/σ(I): 14.3
Reflection shellResolution: 2→2.07 Å / Rmerge(I) obs: 0.197 / Num. unique all: 76643
Reflection
*PLUS
Num. measured all: 744944

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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→20 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2549 3861 5.3 %RANDOM
Rwork0.1757 ---
all0.1751 73036 --
obs-73036 96.4 %-
Displacement parametersBiso mean: 20 Å2
Refinement stepCycle: LAST / Resolution: 2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8436 0 468 1630 10534
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.014
X-RAY DIFFRACTIONp_angle_deg2.9
X-RAY DIFFRACTIONp_angle_d2.9
LS refinement shellResolution: 2→2.09 Å
RfactorNum. reflection
Rfree0.263 440
Rwork0.179 -
obs-8800
Software
*PLUS
Name: REFMAC / Classification: refinement
Refinement
*PLUS
σ(F): 0 / % reflection Rfree: 5.3 % / Rfactor obs: 0.1751
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 20 Å2
Refine LS restraints
*PLUS
Type: p_angle_d / Dev ideal: 2.9

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