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- PDB-1rq1: Structure of Ero1p, Source of Disulfide Bonds for Oxidative Prote... -

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Basic information

Entry
Database: PDB / ID: 1rq1
TitleStructure of Ero1p, Source of Disulfide Bonds for Oxidative Protein Folding in the Cell
ComponentsHypothetical 65.0 kDa protein in COX14-COS3 intergenic region precursor
KeywordsOXIDOREDUCTASE / flavoenzyme / disulfide bonds / CXXCXXC
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 / MIR / Resolution: 2.8 Å
AuthorsGross, E. / Kastner, D.B. / Kaiser, C.A. / Fass, D.
CitationJournal: Cell(Cambridge,Mass.) / Year: 2004
Title: Structure of ero1p, source of disulfide bonds for oxidative protein folding in the cell.
Authors: Gross, E. / Kastner, D.B. / Kaiser, C.A. / Fass, D.
History
DepositionDec 4, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 8, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 30, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / 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_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _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: Hypothetical 65.0 kDa protein in COX14-COS3 intergenic region precursor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,5905
Polymers44,4521
Non-polymers1,1384
Water1,02757
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)106.200, 106.200, 124.300
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number171
Space group name H-MP62

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Components

#1: Protein Hypothetical 65.0 kDa protein in COX14-COS3 intergenic region precursor


Mass: 44452.016 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: YML130C, YM4987.05C / Plasmid: pGEX-4T1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q03103
#2: Chemical ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cd
#3: Chemical ChemComp-NEN / 1-ETHYL-PYRROLIDINE-2,5-DIONE


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


Mass: 785.550 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 57 / 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: 4.55 Å3/Da / Density % sol: 72.97 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.8
Details: cacodylate, cadmium chloride, sodium acetate, pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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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: Feb 15, 2003 / Details: Osmic mirrors
RadiationMonochromator: Osmic mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. all: 19628 / Num. obs: 19520 / % possible obs: 99.4 % / Observed criterion σ(I): -3 / Redundancy: 7.5 % / Biso Wilson estimate: 29.5 Å2 / Rsym value: 0.064 / Net I/σ(I): 19.2

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
SHARPphasing
CNS1refinement
RefinementMethod to determine structure: MIR / Resolution: 2.8→50 Å / σ(F): 0
RfactorNum. reflection
Rfree0.238 1342
Rwork0.206 -
all-19628
obs-19520
Refinement stepCycle: LAST / Resolution: 2.8→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2894 0 64 57 3015
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.752

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