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- PDB-4e0i: Crystal structure of the C30S/C133S mutant of Erv1 from Saccharom... -

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Basic information

Entry
Database: PDB / ID: 4e0i
TitleCrystal structure of the C30S/C133S mutant of Erv1 from Saccharomyces cerevisiae
ComponentsMitochondrial FAD-linked sulfhydryl oxidase ERV1
KeywordsOXIDOREDUCTASE / Flavin-linked sulfhydryl oxidase / Mia40 / oxidation / mitochondrial intermembrane space
Function / homology
Function and homology information


flavin-dependent sulfhydryl oxidase activity / thiol oxidase / thiol oxidase activity / protein import into mitochondrial intermembrane space / mitochondrial intermembrane space / flavin adenine dinucleotide binding / cellular response to oxidative stress / intracellular iron ion homeostasis / mitochondrion
Similarity search - Function
Dihydrolipoamide Transferase - #60 / Sulfhydryl oxidase ALR/ERV / ERV/ALR sulfhydryl oxidase domain / ERV/ALR sulfhydryl oxidase domain / ERV/ALR sulfhydryl oxidase domain superfamily / Erv1 / Alr family / ERV/ALR sulfhydryl oxidase domain profile. / Dihydrolipoamide Transferase / Four Helix Bundle (Hemerythrin (Met), subunit A) / Few Secondary Structures ...Dihydrolipoamide Transferase - #60 / Sulfhydryl oxidase ALR/ERV / ERV/ALR sulfhydryl oxidase domain / ERV/ALR sulfhydryl oxidase domain / ERV/ALR sulfhydryl oxidase domain superfamily / Erv1 / Alr family / ERV/ALR sulfhydryl oxidase domain profile. / Dihydrolipoamide Transferase / Four Helix Bundle (Hemerythrin (Met), subunit A) / Few Secondary Structures / Irregular / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / Mitochondrial FAD-linked sulfhydryl oxidase ERV1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsGuo, P.C. / Ma, J.D. / Jiang, Y.L. / Wang, S.J. / Hu, T.T. / Chen, Y.X. / Zhou, C.Z.
CitationJournal: J.Biol.Chem. / Year: 2012
Title: Structure of yeast sulfhydryl oxidase erv1 reveals electron transfer of the disulfide relay system in the mitochondrial intermembrane space
Authors: Guo, P.C. / Ma, J.D. / Jiang, Y.L. / Wang, S.J. / Bao, Z.Z. / Yu, X.J. / Chen, Y. / Zhou, C.Z.
History
DepositionMar 4, 2012Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Aug 29, 2012Provider: repository / Type: Initial release
Revision 1.1Jan 30, 2013Group: Database references
Revision 1.2Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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 / _struct_ref_seq_dif.details / _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: Mitochondrial FAD-linked sulfhydryl oxidase ERV1
B: Mitochondrial FAD-linked sulfhydryl oxidase ERV1
C: Mitochondrial FAD-linked sulfhydryl oxidase ERV1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,2756
Polymers64,9183
Non-polymers2,3573
Water0
1
A: Mitochondrial FAD-linked sulfhydryl oxidase ERV1
B: Mitochondrial FAD-linked sulfhydryl oxidase ERV1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,8504
Polymers43,2792
Non-polymers1,5712
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7440 Å2
ΔGint-56 kcal/mol
Surface area14980 Å2
MethodPISA
2
C: Mitochondrial FAD-linked sulfhydryl oxidase ERV1
hetero molecules

C: Mitochondrial FAD-linked sulfhydryl oxidase ERV1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,8504
Polymers43,2792
Non-polymers1,5712
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area6520 Å2
ΔGint-51 kcal/mol
Surface area13200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.280, 77.680, 116.230
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21221

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Components

#1: Protein Mitochondrial FAD-linked sulfhydryl oxidase ERV1 / 14 kDa regulatory protein / Essential for respiration and vegetative growth protein 1


Mass: 21639.381 Da / Num. of mol.: 3 / Mutation: C30S,C133S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: s288c / Gene: YGR029W / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P27882, thiol oxidase
#2: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE / Flavin adenine dinucleotide


Mass: 785.550 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM

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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: 2.2 Å3/Da / Density % sol: 44.1 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 15% polyethylene glycol 6000, 0.1M HEPES, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.979 Å
DetectorDetector: CCD / Date: Nov 1, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 3→49.06 Å / Num. all: 11892 / Num. obs: 11797 / % possible obs: 99.2 %
Reflection shellResolution: 3→3.16 Å / % possible all: 98.6

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Processing

Software
NameVersionClassification
HKL-2000data collection
AMoREphasing
REFMAC5.6.0117refinement
HKL-2000data reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4E0H

4e0h


Resolution: 3→46.53 Å / Cor.coef. Fo:Fc: 0.882 / Cor.coef. Fo:Fc free: 0.839 / SU B: 24.351 / SU ML: 0.442 / Cross valid method: THROUGHOUT / ESU R Free: 0.511 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.3041 567 4.8 %RANDOM
Rwork0.25542 ---
obs0.2578 11306 98.93 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 50.73 Å2
Baniso -1Baniso -2Baniso -3
1--0.88 Å20 Å20 Å2
2--6.09 Å20 Å2
3----5.21 Å2
Refinement stepCycle: LAST / Resolution: 3→46.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3250 0 159 0 3409
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.023518
X-RAY DIFFRACTIONr_angle_refined_deg0.9021.9924781
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.8935385
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.49223.92176
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.06115597
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.8581525
X-RAY DIFFRACTIONr_chiral_restr0.0650.2455
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0212683
LS refinement shellResolution: 3→3.078 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.333 36 -
Rwork0.336 726 -
obs--98.58 %

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