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- PDB-3ed3: Crystal Structure of the Yeast Dithiol/Disulfide Oxidoreductase Mpd1p -

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Basic information

Entry
Database: PDB / ID: 3ed3
TitleCrystal Structure of the Yeast Dithiol/Disulfide Oxidoreductase Mpd1p
ComponentsProtein disulfide-isomerase MPD1
KeywordsISOMERASE / thioredoxin-like domain / CXXC / Endoplasmic reticulum / Glycoprotein / Redox-active center
Function / homology
Function and homology information


protein-disulfide reductase (glutathione) activity / protein disulfide-isomerase / fungal-type vacuole / protein disulfide isomerase activity / protein-disulfide reductase activity / cell redox homeostasis / protein folding / endoplasmic reticulum lumen / endoplasmic reticulum
Similarity search - Function
Endoplasmic reticulum targeting sequence. / Thioredoxin / Thioredoxin, conserved site / Thioredoxin family active site. / Thioredoxin domain profile. / Thioredoxin domain / Glutaredoxin / Glutaredoxin / Thioredoxin-like superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / Protein disulfide-isomerase MPD1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2 Å
AuthorsVitu, E. / Greenblatt, H.M. / Fass, D.
CitationJournal: J.Mol.Biol. / Year: 2008
Title: Yeast Mpd1p reveals the structural diversity of the protein disulfide isomerase family
Authors: Vitu, E. / Gross, E. / Greenblatt, H.M. / Sevier, C.S. / Kaiser, C.A. / Fass, D.
History
DepositionSep 2, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 4, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Protein disulfide-isomerase MPD1
B: Protein disulfide-isomerase MPD1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,23815
Polymers68,4592
Non-polymers78013
Water5,242291
1
A: Protein disulfide-isomerase MPD1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,7089
Polymers34,2291
Non-polymers4788
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Protein disulfide-isomerase MPD1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,5316
Polymers34,2291
Non-polymers3015
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)48.157, 92.268, 79.337
Angle α, β, γ (deg.)90.00, 92.23, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Protein disulfide-isomerase MPD1


Mass: 34229.285 Da / Num. of mol.: 2 / Fragment: UNP residues 23-310
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: MPD1 / Plasmid: pET-15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)plysS / References: UniProt: Q12404, protein disulfide-isomerase
#2: Chemical
ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 291 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.57 Å3/Da / Density % sol: 52.19 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.9
Details: 17% PEG4K, 0.2M sodium acetate, 100mM cacodylic acid (pH5.9), 6-10% ethylene glycol, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineTypeIDWavelength (Å)
ROTATING ANODERIGAKU RUH3R11.5418
SYNCHROTRONESRF BM1420.97850, 0.88550
Detector
TypeIDDetectorDateDetails
RIGAKU1IMAGE PLATEJul 15, 2006Osmic mirrors
MAR2CCDNov 10, 2006Osmic mirrors
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2MADMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
11.54181
20.97851
30.88551
ReflectionResolution: 2→50 Å / Num. all: 46859 / Num. obs: 45863 / % possible obs: 97.9 % / Redundancy: 5.8 % / Biso Wilson estimate: 51 Å2 / Rsym value: 0.064 / Net I/σ(I): 17
Reflection shellResolution: 2→2.07 Å / Redundancy: 5.3 % / Mean I/σ(I) obs: 3.3 / Num. unique all: 4648 / Rsym value: 0.676 / % possible all: 94.7

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Processing

Software
NameVersionClassification
SOLVEphasing
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MAD / Resolution: 2→50 Å / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.255 3243 -random
Rwork0.219 ---
all-46859 --
obs-45840 97.8 %-
Refinement stepCycle: LAST / Resolution: 2→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4313 0 52 291 4656
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.284

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