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- PDB-3boa: Crystal structure of yeast protein disulfide isomerase. -

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Basic information

Entry
Database: PDB / ID: 3boa
TitleCrystal structure of yeast protein disulfide isomerase.
ComponentsProtein disulfide-isomerase
KeywordsISOMERASE / Disulfide bond formation / Endoplasmic reticulum / Molecular flexibility / Protein folding / Thioredoxin / Glycoprotein / Redox-active center
Function / homology
Function and homology information


mannosyl-oligosaccharide 1,2-alpha-mannosidase complex / mannose trimming involved in glycoprotein ERAD pathway / Calnexin/calreticulin cycle / protein alpha-1,2-demannosylation / protein disulfide-isomerase / positive regulation of endoplasmic reticulum unfolded protein response / protein disulfide isomerase activity / protein-disulfide reductase activity / response to endoplasmic reticulum stress / unfolded protein binding ...mannosyl-oligosaccharide 1,2-alpha-mannosidase complex / mannose trimming involved in glycoprotein ERAD pathway / Calnexin/calreticulin cycle / protein alpha-1,2-demannosylation / protein disulfide-isomerase / positive regulation of endoplasmic reticulum unfolded protein response / protein disulfide isomerase activity / protein-disulfide reductase activity / response to endoplasmic reticulum stress / unfolded protein binding / protein folding / endoplasmic reticulum lumen / cell surface / endoplasmic reticulum
Similarity search - Function
Protein disulphide isomerase / Thioredoxin-like domain / Endoplasmic reticulum targeting sequence. / Thioredoxin / Thioredoxin, conserved site / Thioredoxin family active site. / Thioredoxin domain profile. / Thioredoxin domain / Glutaredoxin / Glutaredoxin ...Protein disulphide isomerase / Thioredoxin-like domain / 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
Protein disulfide-isomerase
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.7 Å
AuthorsTian, G. / Lennarz, W.J. / Schindelin, H.
CitationJournal: J.Biol.Chem. / Year: 2008
Title: The Catalytic Activity of Protein-disulfide Isomerase Requires a Conformationally Flexible Molecule.
Authors: Tian, G. / Kober, F.X. / Lewandrowski, U. / Sickmann, A. / Lennarz, W.J. / Schindelin, H.
History
DepositionDec 17, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 23, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Aug 30, 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Protein disulfide-isomerase


Theoretical massNumber of molelcules
Total (without water)56,4221
Polymers56,4221
Non-polymers00
Water00
1
A: Protein disulfide-isomerase

A: Protein disulfide-isomerase


Theoretical massNumber of molelcules
Total (without water)112,8432
Polymers112,8432
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_545x,-y-1,-z1
Buried area4640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)116.921, 123.154, 75.721
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 Protein disulfide-isomerase / PDI / Thioredoxin- related glycoprotein 1


Mass: 56421.613 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: W303 / Gene: PDI1, MFP1, TRG1 / Plasmid: pTYB12 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 Codon+ RIL / References: UniProt: P17967, protein disulfide-isomerase

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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: 2.42 Å3/Da / Density % sol: 49.2 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 100mM NaCacodylate 6.5, 0.35M MgCl2, 29% PEG2000 MME, 1mM BaCl2 , VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X26C / Wavelength: 1.1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: May 30, 2004
RadiationMonochromator: Si(111) crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 3.7→50 Å / Num. obs: 6049 / % possible obs: 99.8 % / Redundancy: 5.6 % / Rsym value: 0.092 / Net I/σ(I): 18.3
Reflection shellResolution: 3.7→3.76 Å / Redundancy: 5.5 % / Mean I/σ(I) obs: 2.1 / Rsym value: 0.696 / % possible all: 99.7

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
CBASSdata collection
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2B5E

2b5e


Resolution: 3.7→19.81 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.888 / SU B: 190.152 / SU ML: 1.178 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / ESU R Free: 1.05 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.33984 306 5.1 %RANDOM
Rwork0.23919 ---
obs0.2442 5738 99.95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 168.842 Å2
Baniso -1Baniso -2Baniso -3
1--0.32 Å20 Å20 Å2
2---0.29 Å20 Å2
3---0.61 Å2
Refinement stepCycle: LAST / Resolution: 3.7→19.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3864 0 0 0 3864
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0223954
X-RAY DIFFRACTIONr_bond_other_d0.0020.023428
X-RAY DIFFRACTIONr_angle_refined_deg1.181.9585369
X-RAY DIFFRACTIONr_angle_other_deg0.79838046
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.1475489
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.07926.169201
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.37315656
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.954157
X-RAY DIFFRACTIONr_chiral_restr0.0690.2585
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.024466
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02758
X-RAY DIFFRACTIONr_nbd_refined0.2230.21258
X-RAY DIFFRACTIONr_nbd_other0.1720.24147
X-RAY DIFFRACTIONr_nbtor_refined0.1850.21941
X-RAY DIFFRACTIONr_nbtor_other0.0840.22414
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1810.2147
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0280.22
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1830.242
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1720.278
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1630.27
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.251.53135
X-RAY DIFFRACTIONr_mcbond_other0.0241.5983
X-RAY DIFFRACTIONr_mcangle_it0.29623942
X-RAY DIFFRACTIONr_scbond_it0.32531767
X-RAY DIFFRACTIONr_scangle_it0.5154.51427
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.7→3.793 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.463 24 -
Rwork0.408 411 -
obs--100 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
18.299-4.21984.00595.8035-2.5799.9633-1.097-0.5758-0.01041.3230.7154-0.4082-0.75211.15520.38160.7181-0.0477-0.29520.0071-0.1284-0.3479-66.8744-77.8342-7.3378
26.8031-0.8478-1.008915.60351.260310.18250.36850.27490.00981.9846-0.51271.2943-0.2306-0.91770.1442-0.1713-0.3175-0.0304-0.06190.1482-0.3963-41.1313-74.101513.3367
36.40810.0675-0.315810.5532.75157.31280.3087-0.21260.26450.38840.3982-1.7069-0.17640.0156-0.7068-0.7165-0.1346-0.2374-0.31590.1672-0.2674-23.8723-49.266810.7834
43.6688-2.89873.417711.4917-5.9339.22180.0631-0.27360.25810.3636-0.33670.4245-0.4865-0.45580.2736-0.34890.06980.036-0.13040.0502-0.2724-45.0179-18.91761.299
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA24 - 1406 - 122
2X-RAY DIFFRACTION2AA141 - 240123 - 222
3X-RAY DIFFRACTION3AA241 - 367223 - 349
4X-RAY DIFFRACTION4AA368 - 513350 - 495

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