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- PDB-5zyn: Fumarate reductase -

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Basic information

Entry
Database: PDB / ID: 5zyn
TitleFumarate reductase
ComponentsFumarate reductase 2
KeywordsOXIDOREDUCTASE / Fumarate reductase
Function / homology
Function and homology information


fumarate reductase (NADH) / fumarate reductase (NADH) activity / FAD metabolic process / protein folding in endoplasmic reticulum / FMN binding / endoplasmic reticulum / mitochondrion
Similarity search - Function
Flavocytochrome c / Succinate dehydrogenase/fumarate reductase flavoprotein, catalytic domain superfamily / FAD-dependent oxidoreductase 2, FAD binding domain / FAD binding domain / FAD/NAD(P)-binding domain superfamily
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / FLAVIN MONONUCLEOTIDE / SUCCINIC ACID / Fumarate reductase 2
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsPark, H.H. / Kim, C.M.
CitationJournal: Nat Commun / Year: 2018
Title: Molecular basis of maintaining an oxidizing environment under anaerobiosis by soluble fumarate reductase.
Authors: Kim, S. / Kim, C.M. / Son, Y.J. / Choi, J.Y. / Siegenthaler, R.K. / Lee, Y. / Jang, T.H. / Song, J. / Kang, H. / Kaiser, C.A. / Park, H.H.
History
DepositionMay 25, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 3, 2018Provider: repository / Type: Initial release
Revision 1.1Dec 12, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.name
Revision 1.2Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Fumarate reductase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,9564
Polymers51,5961
Non-polymers1,3603
Water5,026279
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2550 Å2
ΔGint-19 kcal/mol
Surface area18700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.882, 109.321, 49.932
Angle α, β, γ (deg.)90.00, 112.25, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Fumarate reductase 2 / FRDS2 / NADH-dependent fumarate reductase / Osmotic sensitivity protein 1 / Soluble fumarate ...FRDS2 / NADH-dependent fumarate reductase / Osmotic sensitivity protein 1 / Soluble fumarate reductase / mitochondrial isozyme


Mass: 51595.676 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: OSM1, YJR051W, J1659 / Production host: Escherichia coli (E. coli) / References: UniProt: P21375, fumarate reductase (NADH)
#2: Chemical ChemComp-SIN / SUCCINIC ACID


Mass: 118.088 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H6O4
#3: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE


Mass: 456.344 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H21N4O9P
#4: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 279 / 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: 2.15 Å3/Da / Density % sol: 42.75 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 22% PEG 3350, 0.1M BIS TRIS pH 5.5

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.987 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 1, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 1.75→50 Å / Num. obs: 164160 / % possible obs: 94.5 % / Redundancy: 4 % / Rmerge(I) obs: 0.061 / Net I/σ(I): 33.1
Reflection shellResolution: 1.75→1.78 Å / Rmerge(I) obs: 0.296 / Num. unique obs: 2176

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1QJD

1qjd


Resolution: 1.75→26.499 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.25 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.239 1989 4.82 %
Rwork0.1884 --
obs0.1909 41288 94.25 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.75→26.499 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3617 0 93 279 3989
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073770
X-RAY DIFFRACTIONf_angle_d1.1355104
X-RAY DIFFRACTIONf_dihedral_angle_d14.4521386
X-RAY DIFFRACTIONf_chiral_restr0.044588
X-RAY DIFFRACTIONf_plane_restr0.005642
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7503-1.79410.2651440.20392935X-RAY DIFFRACTION99
1.7941-1.84260.27131560.21112979X-RAY DIFFRACTION100
1.8426-1.89680.34871370.26662922X-RAY DIFFRACTION98
1.8968-1.9580.39191480.30632774X-RAY DIFFRACTION94
1.958-2.0280.30541510.22712971X-RAY DIFFRACTION99
2.028-2.10910.25671440.20362986X-RAY DIFFRACTION100
2.1091-2.20510.27391550.20622956X-RAY DIFFRACTION100
2.2051-2.32130.3136880.22761778X-RAY DIFFRACTION60
2.3213-2.46660.27021550.1972961X-RAY DIFFRACTION100
2.4666-2.65690.24151420.19492976X-RAY DIFFRACTION100
2.6569-2.9240.23451560.19713018X-RAY DIFFRACTION100
2.924-3.34640.19971510.17942968X-RAY DIFFRACTION100
3.3464-4.21330.20451080.15252168X-RAY DIFFRACTION73
4.2133-26.50240.17351540.13822907X-RAY DIFFRACTION96
Refinement TLS params.Method: refined / Origin x: 12.5461 Å / Origin y: 27.1073 Å / Origin z: 5.5995 Å
111213212223313233
T0.1073 Å20.016 Å20.0052 Å2-0.1235 Å2-0.0096 Å2--0.1076 Å2
L1.0277 °2-0.1429 °2-0.1578 °2-0.9241 °2-0.2169 °2--1.2642 °2
S-0.0708 Å °0.0072 Å °-0.0538 Å °-0.0197 Å °-0.0026 Å °-0.015 Å °0.1349 Å °0.1938 Å °0.0441 Å °
Refinement TLS groupSelection details: all

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