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- PDB-6ku6: OSM1 mutant - R326A -

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Basic information

Entry
Database: PDB / ID: 6ku6
TitleOSM1 mutant - R326A
ComponentsFumarate reductase 2
KeywordsOXIDOREDUCTASE / Fumarase reductase mutant R326A
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 / SUCCINIC ACID / Fumarate reductase 2
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.007 Å
AuthorsPark, H.H. / Kim, C.M.
Funding support Korea, Republic Of, 1items
OrganizationGrant numberCountry
National Research Foundation (Korea) Korea, Republic Of
CitationJournal: Crystals / Year: 2019
Title: Crystal Structure of the Active Site Mutant Form of Soluble Fumarate Reductase, Osm1
Authors: Kim, C.M. / Kwon, S. / Jung, K.H. / Park, H.H.
History
DepositionAug 30, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 8, 2020Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Fumarate reductase 2
H: Fumarate reductase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,8266
Polymers103,0192
Non-polymers1,8074
Water10,791599
1
B: Fumarate reductase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,4133
Polymers51,5101
Non-polymers9042
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1800 Å2
ΔGint-4 kcal/mol
Surface area18570 Å2
MethodPISA
2
H: Fumarate reductase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,4133
Polymers51,5101
Non-polymers9042
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1800 Å2
ΔGint-4 kcal/mol
Surface area18630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.924, 109.924, 77.142
Angle α, β, γ (deg.)90.000, 98.520, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain B
21chain H

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111chain BB1
211chain HH2

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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: 51509.559 Da / Num. of mol.: 2 / Mutation: R326A
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-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: FAD*YM
#3: Chemical ChemComp-SIN / SUCCINIC ACID


Mass: 118.088 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H6O4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 599 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.11 Å3/Da / Density % sol: 41.8 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 5.5 / Details: PEG 3350, BIS TRIS pH 5.5

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Data collection

DiffractionMean temperature: 104.15 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.9795 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jun 13, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.007→38.145 Å / Num. obs: 56568 / % possible obs: 99.9 % / Redundancy: 6.5 % / Rsym value: 0.156 / Net I/σ(I): 15.0625
Reflection shellResolution: 2.007→2.03 Å / Num. unique obs: 639 / Rsym value: 0.491

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.007→38.145 Å / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 30.53
RfactorNum. reflection% reflection
Rfree0.2505 1996 3.54 %
Rwork0.1995 --
obs0.2013 56437 98.77 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 58.83 Å2 / Biso mean: 24.3615 Å2 / Biso min: 9.89 Å2
Refinement stepCycle: final / Resolution: 2.007→38.145 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7222 0 122 599 7943
Biso mean--20.81 29.48 -
Num. residues----942
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11B4492X-RAY DIFFRACTION6.373TORSIONAL
12H4492X-RAY DIFFRACTION6.373TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.0072-2.05740.38321250.2679340687
2.0574-2.1130.32271430.24943897100
2.113-2.17520.26811440.23483928100
2.1752-2.24540.32071440.2283905100
2.2454-2.32560.27331440.2243941100
2.3256-2.41880.26661440.22423918100
2.4188-2.52880.28771430.21283910100
2.5288-2.66210.24671440.2173931100
2.6621-2.82880.27471430.2153911100
2.8288-3.04720.25781450.20493941100
3.0472-3.35370.26121440.20233925100
3.3537-3.83850.21411450.17633934100
3.8385-4.83460.19061450.15543967100
4.8346-38.1450.21751430.1746392798

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