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- PDB-3ahr: Inactive human Ero1 -

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Basic information

Entry
Database: PDB / ID: 3ahr
TitleInactive human Ero1
ComponentsERO1-like protein alpha
KeywordsOXIDOREDUCTASE / disulfide bond / PDI / redox / ER
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 maturation by protein folding / response to temperature stimulus / Detoxification of Reactive Oxygen Species / chaperone cofactor-dependent protein refolding / protein-disulfide reductase activity / intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress / brown fat cell differentiation ...Oxidoreductases; Acting on a sulfur group of donors; With a disulfide as acceptor / thiol oxidase activity / protein folding in endoplasmic reticulum / protein maturation by protein folding / response to temperature stimulus / Detoxification of Reactive Oxygen Species / chaperone cofactor-dependent protein refolding / protein-disulfide reductase activity / intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress / brown fat cell differentiation / endoplasmic reticulum unfolded protein response / release of sequestered calcium ion into cytosol / FAD binding / response to endoplasmic reticulum stress / extracellular matrix organization / cell redox homeostasis / protein modification process / Golgi lumen / protein folding / cellular response to hypoxia / response to oxidative stress / oxidoreductase activity / endoplasmic reticulum lumen / intracellular membrane-bounded organelle / dendrite / endoplasmic reticulum membrane / endoplasmic reticulum / extracellular space / membrane
Similarity search - Function
Endoplasmic reticulum oxidoreductin 1 / ERO1-like superfamily / Endoplasmic Reticulum Oxidoreductin 1 (ERO1)
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / ERO1-like protein alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.07 Å
AuthorsInaba, K. / Sitia, R. / Suzuki, M.
CitationJournal: Embo J. / Year: 2010
Title: Crystal structures of human Ero1-alpha reveal the mechanisms of regulated and targeted oxidation of PDI
Authors: Inaba, K. / Masui, S. / Iida, H. / Vavassori, S. / Sitia, R. / Suzuki, M.
History
DepositionApr 26, 2010Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 22, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ERO1-like protein alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,9582
Polymers54,1731
Non-polymers7861
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)54.698, 139.094, 143.491
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222

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Components

#1: Protein ERO1-like protein alpha / ERO1-L-alpha / ERO1-L / Oxidoreductin-1-L-alpha / Endoplasmic oxidoreductin-1-like protein


Mass: 54172.828 Da / Num. of mol.: 1 / Mutation: C99A, C104A, C166A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: Ero1-Lalpha / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q96HE7, Oxidoreductases; Acting on a sulfur group of donors; With a disulfide as acceptor
#2: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE / Flavin adenine dinucleotide


Mass: 785.550 Da / Num. of mol.: 1 / 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: 2.52 Å3/Da / Density % sol: 51.17 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 8
Details: 20% PEG1500, 80mM imidazole pH8.0, VAPOR DIFFUSION, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Dec 4, 2009 / Details: mirror
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 3.07→36.01 Å / Num. obs: 10434 / % possible obs: 98.7 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.063 / Rsym value: 0.074 / Net I/σ(I): 13.8
Reflection shellResolution: 3.07→3.24 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.428 / Mean I/σ(I) obs: 2.9 / Rsym value: 0.503 / % possible all: 93.1

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Processing

Software
NameVersionClassification
BSSdata collection
MOLREPphasing
REFMAC5.5.0109refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1RP4

1rp4


Resolution: 3.07→36.01 Å / Cor.coef. Fo:Fc: 0.922 / Cor.coef. Fo:Fc free: 0.845 / SU B: 20.998 / SU ML: 0.389 / Cross valid method: THROUGHOUT / ESU R Free: 0.532 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.30253 572 5.5 %RANDOM
Rwork0.22352 ---
obs0.22779 9831 98.22 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 67.368 Å2
Baniso -1Baniso -2Baniso -3
1--0.14 Å20 Å20 Å2
2--0.24 Å20 Å2
3----0.1 Å2
Refinement stepCycle: LAST / Resolution: 3.07→36.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3016 0 53 0 3069
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0223153
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6231.9754262
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3385358
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.49623.795166
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.48315556
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.7611523
X-RAY DIFFRACTIONr_chiral_restr0.10.2441
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0212397
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.8461.51801
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.61322899
X-RAY DIFFRACTIONr_scbond_it1.85531352
X-RAY DIFFRACTIONr_scangle_it3.2334.51363
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.072→3.151 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.368 30 -
Rwork0.26 626 -
obs--86.43 %

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