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- PDB-3m31: Structure of the C150A/C295A mutant of S. cerevisiae Ero1p -

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Basic information

Entry
Database: PDB / ID: 3m31
TitleStructure of the C150A/C295A mutant of S. cerevisiae Ero1p
ComponentsEndoplasmic oxidoreductin-1
KeywordsOXIDOREDUCTASE / disulfide mutant / Disulfide bond / Electron transport / Endoplasmic reticulum / FAD / Flavoprotein / Glycoprotein / Membrane / Redox-active center / Transport
Function / homology
Function and homology information


Oxidoreductases; Acting on a sulfur group of donors; With a disulfide as acceptor / thiol oxidase activity / protein folding in endoplasmic reticulum / protein-disulfide reductase activity / FAD binding / endoplasmic reticulum membrane / endoplasmic reticulum
Similarity search - Function
Endoplasmic reticulum oxidoreductin 1 / ERO1-like superfamily / Endoplasmic Reticulum Oxidoreductin 1 (ERO1)
Similarity search - Domain/homology
: / FLAVIN-ADENINE DINUCLEOTIDE / 1-ETHYL-PYRROLIDINE-2,5-DIONE / Endoplasmic oxidoreductin-1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsHeldman, N. / Fass, D.
CitationJournal: Protein Sci. / Year: 2010
Title: Steps in reductive activation of the disulfide-generating enzyme Ero1p
Authors: Heldman, N. / Vonshak, O. / Sevier, C.S. / Vitu, E. / Mehlman, T. / Fass, D.
History
DepositionMar 8, 2010Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 3, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 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
Revision 1.3Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Endoplasmic oxidoreductin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,7554
Polymers44,7301
Non-polymers1,0253
Water3,621201
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Endoplasmic oxidoreductin-1
hetero molecules

A: Endoplasmic oxidoreductin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,5118
Polymers89,4612
Non-polymers2,0506
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_565x,-y+1,-z1
Buried area2350 Å2
ΔGint-3 kcal/mol
Surface area31330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.441, 132.772, 102.676
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Endoplasmic oxidoreductin-1 / Ero1p / Endoplasmic oxidoreductase protein 1


Mass: 44730.305 Da / Num. of mol.: 1 / Fragment: residues in UNP 56-424 / Mutation: C150A, C295A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: ERO1 / Plasmid: modified pGEX-4T1 / Production host: Escherichia coli (E. coli) / Strain (production host): Origami B(DE3) plysS
References: UniProt: Q03103, Oxidoreductases; Acting on a sulfur group of donors; With a disulfide as acceptor
#2: Chemical ChemComp-NEN / 1-ETHYL-PYRROLIDINE-2,5-DIONE


Mass: 127.141 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H9NO2
#3: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#4: Chemical ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cd
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 201 / 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: 2.8 Å3/Da / Density % sol: 56.04 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.2
Details: 100mM cacodylic acid, 10mM cadmium sulfate, 2% methanol, 2% ethanol, 1.2M sodium acetate, pH 6.2, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-3
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 1.85→50 Å / Num. all: 43123 / Num. obs: 42677 / % possible obs: 99 % / Redundancy: 4.9 % / Rsym value: 0.037 / Net I/σ(I): 15.4
Reflection shellResolution: 1.85→1.92 Å / Redundancy: 3.3 % / Mean I/σ(I) obs: 2.2 / Num. unique all: 4231 / Rsym value: 0.521 / % possible all: 92.1

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1RP4 after removal of residues 146 to 166 and 291 to 302

1rp4


Resolution: 1.85→50 Å / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.238 2864 -random
Rwork0.209 ---
obs-42641 98.8 %-
Refinement stepCycle: LAST / Resolution: 1.85→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2899 0 63 201 3163
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.314

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