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- PDB-1jr8: Crystal Structure of Erv2p -

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Basic information

Entry
Database: PDB / ID: 1jr8
TitleCrystal Structure of Erv2p
ComponentsErv2 PROTEIN, mitochondrial
KeywordsOXIDOREDUCTASE / FAD / sulfhydryl oxidase / helical bundle / CXXC
Function / homology
Function and homology information


flavin-dependent sulfhydryl oxidase activity / thiol oxidase / thiol oxidase activity / fungal-type vacuole / fungal-type vacuole membrane / flavin adenine dinucleotide binding / endoplasmic reticulum membrane / mitochondrion
Similarity search - Function
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. / Four Helix Bundle (Hemerythrin (Met), subunit A) / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / FAD-linked sulfhydryl oxidase ERV2
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.5 Å
AuthorsGross, E. / Sevier, C.S. / Vala, A. / Kaiser, C.A. / Fass, D.
CitationJournal: Nat.Struct.Biol. / Year: 2002
Title: A new FAD-binding fold and intersubunit disulfide shuttle in the thiol oxidase Erv2p.
Authors: Gross, E. / Sevier, C.S. / Vala, A. / Kaiser, C.A. / Fass, D.
History
DepositionAug 13, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 28, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Erv2 PROTEIN, mitochondrial
B: Erv2 PROTEIN, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,6204
Polymers27,0492
Non-polymers1,5712
Water5,080282
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5180 Å2
ΔGint-36 kcal/mol
Surface area10740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.640, 45.150, 53.840
Angle α, β, γ (deg.)90.00, 100.15, 90.00
Int Tables number4
Space group name H-MP1211
DetailsThe biological assembly is the dimer found in the asymmetric unit

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Components

#1: Protein Erv2 PROTEIN, mitochondrial / Erv2p sulfhydryl oxidase


Mass: 13524.354 Da / Num. of mol.: 2 / Fragment: protease-resistant domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: ERV2 / Plasmid: pAED4 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 plysS / References: UniProt: Q12284
#2: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 282 / 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: 2.11 Å3/Da / Density % sol: 41.61 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.2
Details: PEG 1000, sodium cacodylate, DMSO, glycerol, pH 6.2, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
Details: used seeding
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
10.1 Mcacodylic acid1reservoirpH6.2
210 mM1reservoirCoCl2
322 %(w/v)PEG80001reservoir

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11201
21001
Diffraction source
SourceSiteBeamlineTypeIDWavelength (Å)
ROTATING ANODERIGAKU RU30011.5418
SYNCHROTRONESRF ID14-420.9797, 0.9794, 0.9393
Detector
TypeIDDetectorDateDetails
RIGAKU RAXIS IV1IMAGE PLATEJun 15, 2001osmic mirrors
ADSC QUANTUM 42CCDJun 4, 2001
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Ni filterSINGLE WAVELENGTHMx-ray1
2Si(111) crystalsMADMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
11.54181
20.97971
30.97941
40.93931
ReflectionResolution: 1.5→50 Å / Num. all: 36251 / Num. obs: 36002 / % possible obs: 99.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.6 % / Biso Wilson estimate: 19.7 Å2 / Rmerge(I) obs: 0.047 / Net I/σ(I): 32.7
Reflection shellResolution: 1.5→1.55 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.265 / Mean I/σ(I) obs: 6.2 / Num. unique all: 3591 / % possible all: 98.2
Reflection
*PLUS
% possible obs: 99.4 %
Reflection shell
*PLUS
% possible obs: 98.2 %

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
CNSrefinement
RefinementMethod to determine structure: MAD / Resolution: 1.5→50 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.233 2517 -random
Rwork0.208 ---
all-36235 --
obs-35984 99.3 %-
Refinement stepCycle: LAST / Resolution: 1.5→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1724 0 106 282 2112
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.78
Software
*PLUS
Name: CNS / Classification: refinement
Refinement
*PLUS
Highest resolution: 1.5 Å / Lowest resolution: 50 Å / σ(F): 0 / % reflection Rfree: 7 % / Rfactor obs: 0.208
Solvent computation
*PLUS
Displacement parameters
*PLUS

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