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- PDB-3wt1: Crystal structure of the b'-a' domain of thermophilic fungal prot... -

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Basic information

Entry
Database: PDB / ID: 3wt1
TitleCrystal structure of the b'-a' domain of thermophilic fungal protein disulfide isomerase (reduced form)
ComponentsProtein disulfide-isomerase
KeywordsISOMERASE / THIOREDOXIN FOLD / DISULFIDE BOND / ENDOPLASMIC RETICULUM / REDOX-ACTIVE CENTER / thioredoxin / oxidoreductase
Function / homology
Function and homology information


protein disulfide-isomerase / protein disulfide isomerase activity / response to endoplasmic reticulum stress / protein folding / endoplasmic reticulum lumen / cell surface
Similarity search - Function
Protein disulphide isomerase / Thioredoxin-like domain / Disulphide isomerase / Endoplasmic reticulum targeting sequence. / Thioredoxin / Thioredoxin, conserved site / Thioredoxin family active site. / Thioredoxin domain profile. / Thioredoxin domain / Glutaredoxin ...Protein disulphide isomerase / Thioredoxin-like domain / Disulphide isomerase / 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 speciesHumicola insolens (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsInagaki, K. / Satoh, T. / Itoh, S.G. / Okumura, H. / Kato, K.
CitationJournal: Chem.Phys.Lett. / Year: 2015
Title: Redox-dependent conformational transition of catalytic domain of protein disulfide isomerase indicated by crystal structure-based molecular dynamics simulation
Authors: Inagaki, K. / Satoh, T. / Itoh, S.G. / Okumura, H. / Kato, K.
History
DepositionApr 2, 2014Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 26, 2014Provider: repository / Type: Initial release
Revision 1.1Dec 3, 2014Group: Database references
Revision 1.2Dec 31, 2014Group: Database references
Revision 1.3Nov 8, 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_ncs_dom_lim / 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_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_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: Protein disulfide-isomerase
B: Protein disulfide-isomerase
C: Protein disulfide-isomerase
D: Protein disulfide-isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)108,4238
Polymers108,0554
Non-polymers3684
Water4,720262
1
A: Protein disulfide-isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,1062
Polymers27,0141
Non-polymers921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Protein disulfide-isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,1062
Polymers27,0141
Non-polymers921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Protein disulfide-isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,1062
Polymers27,0141
Non-polymers921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Protein disulfide-isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,1062
Polymers27,0141
Non-polymers921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)65.77, 67.75, 70.25
Angle α, β, γ (deg.)105.92, 113.13, 96.59
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14B
24C
15B
25D
16C
26D

NCS domain segments:

Component-ID: 0 / Beg auth comp-ID: PRO / Beg label comp-ID: PRO / End auth comp-ID: ALA / End label comp-ID: ALA / Refine code: 0

Dom-IDEns-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11AA208 - 4486 - 246
21BB208 - 4486 - 246
12AA208 - 4486 - 246
22CC208 - 4486 - 246
13AA208 - 4486 - 246
23DD208 - 4486 - 246
14BB208 - 4496 - 247
24CC208 - 4496 - 247
15BB208 - 4496 - 247
25DD208 - 4496 - 247
16CC208 - 4496 - 247
26DD208 - 4496 - 247

NCS ensembles :
ID
1
2
3
4
5
6

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Components

#1: Protein
Protein disulfide-isomerase / / PDI


Mass: 27013.658 Da / Num. of mol.: 4 / Fragment: UNP residues 278-469
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Humicola insolens (fungus) / Plasmid: pGEX6P-1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P55059, protein disulfide-isomerase
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 262 / 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: 2.48 Å3/Da / Density % sol: 50.39 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 36% PEG2000MME, 100mM sodium acetate pH 4.6, 200mM ammonium sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 3, 2012
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.85→50 Å / Num. all: 88599 / Num. obs: 81751 / % possible obs: 92.3 % / Observed criterion σ(I): -3 / Redundancy: 2.1 % / Biso Wilson estimate: 68.4 Å2 / Rmerge(I) obs: 0.055 / Net I/σ(I): 26.2
Reflection shellResolution: 1.85→1.88 Å / Redundancy: 2 % / Rmerge(I) obs: 0.378 / Mean I/σ(I) obs: 1.5 / Num. unique all: 3648 / % possible all: 81.7

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Processing

Software
NameVersionClassification
HKL-2000data collection
MOLREPphasing
REFMAC5.7.0029refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2KP1

2kp1


Resolution: 1.85→20 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.937 / SU B: 6.001 / SU ML: 0.166 / Cross valid method: THROUGHOUT / ESU R: 0.189 / ESU R Free: 0.171 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.278 4085 5 %RANDOM
Rwork0.238 ---
obs0.24 77551 92.09 %-
all-81751 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 41.453 Å2
Baniso -1Baniso -2Baniso -3
1-0.07 Å2-3.18 Å2-1.43 Å2
2--4.08 Å20.26 Å2
3----1.9 Å2
Refinement stepCycle: LAST / Resolution: 1.85→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7522 0 24 262 7808
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.027741
X-RAY DIFFRACTIONr_bond_other_d0.0070.027432
X-RAY DIFFRACTIONr_angle_refined_deg1.6721.97610485
X-RAY DIFFRACTIONr_angle_other_deg1.361317260
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1055974
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.65725.824340
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.795151319
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.0051517
X-RAY DIFFRACTIONr_chiral_restr0.0930.21153
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0218716
X-RAY DIFFRACTIONr_gen_planes_other0.0060.021593
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A142990.1
12B142990.1
21A142920.11
22C142920.11
31A141630.11
32D141630.11
41B142180.11
42C142180.11
51B140440.12
52D140440.12
61C141320.12
62D141320.12
LS refinement shellResolution: 1.85→1.898 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.411 276 -
Rwork0.412 4984 -
obs--81.05 %

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