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- PDB-4tve: Structure Of the First Two Thioredoxin Domains of Naumovozyma dai... -

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Basic information

Entry
Database: PDB / ID: 4tve
TitleStructure Of the First Two Thioredoxin Domains of Naumovozyma dairenensis Eps1p
ComponentsNaumovozyma dairenensis Eps1p
KeywordsISOMERASE / protein disulfide isomerase / thioredoxin / endoplasmic reticulum / oxidoreductase
Function / homology
Function and homology information


protein retention in ER lumen / protein-disulfide reductase (glutathione) activity / protein disulfide isomerase activity / : / unfolded protein binding / membrane => GO:0016020 / endoplasmic reticulum membrane
Similarity search - Function
Thioredoxin / Thioredoxin domain profile. / Thioredoxin domain / Glutaredoxin / Glutaredoxin / Thioredoxin-like superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Thioredoxin domain-containing protein
Similarity search - Component
Biological speciesNaumovozyma dairenensis (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsDeborah, F. / Biran, S.
Funding supportEuropean Union, Israel, 2items
OrganizationGrant numberCountry
European Research Council (ERC)310649European Union
Kimmel Center for Macromolecular Assemblies Israel
CitationJournal: Plos One / Year: 2014
Title: The eps1p protein disulfide isomerase conserves classic thioredoxin superfamily amino Acid motifs but not their functional geometries.
Authors: Biran, S. / Gat, Y. / Fass, D.
History
DepositionJun 26, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 17, 2014Provider: repository / Type: Initial release
Revision 1.1Jul 27, 2016Group: Data collection
Revision 1.2Jan 8, 2020Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_oper_list
Item: _pdbx_audit_support.country / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Sep 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Naumovozyma dairenensis Eps1p


Theoretical massNumber of molelcules
Total (without water)31,5551
Polymers31,5551
Non-polymers00
Water6,323351
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area14170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.678, 63.584, 119.207
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Naumovozyma dairenensis Eps1p


Mass: 31554.703 Da / Num. of mol.: 1 / Fragment: UNP residues 32-294
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Naumovozyma dairenensis (fungus)
Strain: ATCC 10597 / BCRC 20456 / CBS 421 / NBRC 0211 / NRRL Y-12639
Gene: NDAI0B01070, NDAI_0B01070 / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): Origami B / References: UniProt: G0W5T0, EC: 5.4.3.1
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 351 / 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: 2.56 Å3/Da / Density % sol: 52.01 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 25% w/v PEG 8,000, 0.1 M MES buffer, pH 6.0, 0.2 M calcium acetate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.9763 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 14, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 30298 / % possible obs: 97.79 % / Redundancy: 8.2 % / Net I/σ(I): 9.8
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 8.1 % / Mean I/σ(I) obs: 2.9 / % possible all: 92.8

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.8.4_1496)refinement
HKL-2000HKL2000_704data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2B5E, 3T59

2b5e

3t59


Resolution: 1.8→40.181 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 21.65 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2117 2167 7.15 %
Rwork0.1731 --
obs0.1759 30292 97.77 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.8→40.181 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2101 0 0 351 2452
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072194
X-RAY DIFFRACTIONf_angle_d0.9792971
X-RAY DIFFRACTIONf_dihedral_angle_d12.476824
X-RAY DIFFRACTIONf_chiral_restr0.043317
X-RAY DIFFRACTIONf_plane_restr0.004389
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.840.25561320.21551720X-RAY DIFFRACTION91
1.84-1.8860.26461520.20691797X-RAY DIFFRACTION97
1.886-1.9370.29271300.19951873X-RAY DIFFRACTION97
1.937-1.9940.24771180.19681837X-RAY DIFFRACTION97
1.994-2.05830.25021450.19011854X-RAY DIFFRACTION98
2.0583-2.13190.26441440.17971871X-RAY DIFFRACTION98
2.1319-2.21720.24881370.18161873X-RAY DIFFRACTION99
2.2172-2.31810.24571420.18251872X-RAY DIFFRACTION99
2.3181-2.44030.2041240.17081883X-RAY DIFFRACTION98
2.4403-2.59320.19381660.17871861X-RAY DIFFRACTION99
2.5932-2.79340.18381680.17861871X-RAY DIFFRACTION99
2.7934-3.07440.2151520.17511925X-RAY DIFFRACTION99
3.0744-3.51910.19251330.16391945X-RAY DIFFRACTION99
3.5191-4.43270.1971730.15361923X-RAY DIFFRACTION99
4.4327-40.19060.18571510.16172020X-RAY DIFFRACTION97

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