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- PDB-1jra: Crystal Structure of Erv2p -

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Basic information

Entry
Database: PDB / ID: 1jra
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 / regulation of protein folding in endoplasmic reticulum / thiol oxidase / thiol oxidase activity / fungal-type vacuole / fungal-type vacuole membrane / flavin adenine dinucleotide binding / endoplasmic reticulum membrane / endoplasmic reticulum
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 / MOLECULAR REPLACEMENT / Resolution: 2 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
Revision 1.3Aug 16, 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_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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
C: ERV2 PROTEIN, MITOCHONDRIAL
D: ERV2 PROTEIN, MITOCHONDRIAL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,2408
Polymers54,0974
Non-polymers3,1424
Water5,188288
1
A: ERV2 PROTEIN, MITOCHONDRIAL
B: ERV2 PROTEIN, MITOCHONDRIAL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,6204
Polymers27,0492
Non-polymers1,5712
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5090 Å2
ΔGint-33 kcal/mol
Surface area10860 Å2
MethodPISA
2
C: ERV2 PROTEIN, MITOCHONDRIAL
D: ERV2 PROTEIN, MITOCHONDRIAL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,6204
Polymers27,0492
Non-polymers1,5712
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4850 Å2
ΔGint-33 kcal/mol
Surface area10590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.630, 66.810, 60.380
Angle α, β, γ (deg.)90.00, 91.44, 90.00
Int Tables number4
Space group name H-MP1211
DetailsThe biological assembly is a dimer. The asymmetric unit contains two dimers.

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Components

#1: Protein
ERV2 PROTEIN, MITOCHONDRIAL / Erv2p sulfhydryl oxidase


Mass: 13524.354 Da / Num. of mol.: 4 / 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.: 4 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 288 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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 Å3/Da / Density % sol: 38.44 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.2
Details: PEG 8000, sodium cacodylate, magnesium chloride, pH 6.2, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
10.1 Mcacodylic acid1reservoirpH6.2
250 mM1reservoirMgCl2
332 %(w/v)PEG80001reservoir

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Nov 21, 2000 / Details: osmic mirrors
RadiationMonochromator: Ni / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→20 Å / Num. all: 28911 / Num. obs: 28807 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.3 % / Biso Wilson estimate: 20.9 Å2 / Rmerge(I) obs: 0.082 / Net I/σ(I): 15.1
Reflection shellResolution: 2→2.07 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.461 / Mean I/σ(I) obs: 4.5 / Num. unique all: 2869 / % possible all: 98.3
Reflection
*PLUS
% possible obs: 99.8 %
Reflection shell
*PLUS
% possible obs: 98.3 %

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNSrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1JR8 prior to refinement

1jr8


Resolution: 2→20 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.233 1995 -random
Rwork0.196 ---
all-28911 --
obs-28897 99.5 %-
Refinement stepCycle: LAST / Resolution: 2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3444 0 212 288 3944
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.21
Software
*PLUS
Name: CNS / Classification: refinement
Refinement
*PLUS
Highest resolution: 2 Å / Lowest resolution: 20 Å / Num. reflection obs: 26812 / σ(F): 0 / % reflection Rfree: 7 % / Rfactor obs: 0.196
Solvent computation
*PLUS
Displacement parameters
*PLUS

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