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- PDB-4el1: Crystal structure of oxidized hPDI (abb'xa') -

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Basic information

Entry
Database: PDB / ID: 4el1
TitleCrystal structure of oxidized hPDI (abb'xa')
ComponentsProtein disulfide-isomerase
KeywordsCHAPERONE / abb'a' domains / "CGHC" active sites / Horseshoe shape / enzyme / a redox-regulated chaperone / Endoplasmic reticulum
Function / homology
Function and homology information


regulation of oxidative stress-induced intrinsic apoptotic signaling pathway / procollagen-proline 4-dioxygenase complex / VLDL assembly / insulin processing / procollagen-proline 4-dioxygenase activity / interleukin-23-mediated signaling pathway / LDL remodeling / thiol oxidase activity / protein disulfide-isomerase / peptidyl-proline hydroxylation to 4-hydroxy-L-proline ...regulation of oxidative stress-induced intrinsic apoptotic signaling pathway / procollagen-proline 4-dioxygenase complex / VLDL assembly / insulin processing / procollagen-proline 4-dioxygenase activity / interleukin-23-mediated signaling pathway / LDL remodeling / thiol oxidase activity / protein disulfide-isomerase / peptidyl-proline hydroxylation to 4-hydroxy-L-proline / endoplasmic reticulum chaperone complex / Chylomicron assembly / protein folding in endoplasmic reticulum / Collagen biosynthesis and modifying enzymes / Interleukin-23 signaling / interleukin-12-mediated signaling pathway / cellular response to interleukin-7 / Interleukin-12 signaling / Insulin processing / protein disulfide isomerase activity / Detoxification of Reactive Oxygen Species / positive regulation of cell adhesion / protein-disulfide reductase activity / endoplasmic reticulum-Golgi intermediate compartment / endoplasmic reticulum to Golgi vesicle-mediated transport / positive regulation of substrate adhesion-dependent cell spreading / response to endoplasmic reticulum stress / Post-translational protein phosphorylation / Hedgehog ligand biogenesis / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / melanosome / integrin binding / protein folding / lamellipodium / actin binding / cellular response to hypoxia / positive regulation of viral entry into host cell / cytoskeleton / protein heterodimerization activity / endoplasmic reticulum lumen / external side of plasma membrane / focal adhesion / enzyme binding / endoplasmic reticulum / protein-containing complex / RNA binding / extracellular exosome / extracellular region / cytosol
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 speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.883 Å
AuthorsWang, C. / Li, W. / Ren, J. / Ke, H. / Gong, W. / Feng, W. / Wang, C.-C.
CitationJournal: Antioxid Redox Signal / Year: 2013
Title: Structural insights into the redox-regulated dynamic conformations of human protein disulfide isomerase
Authors: Wang, C. / Li, W. / Ren, J. / Fang, J. / Ke, H. / Gong, W. / Feng, W. / Wang, C.-C.
History
DepositionApr 10, 2012Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 10, 2013Provider: repository / Type: Initial release
Revision 1.1Jul 3, 2013Group: Database references
Revision 1.2Nov 8, 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

Downloads & links

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Assembly

Deposited unit
A: Protein disulfide-isomerase
B: Protein disulfide-isomerase


Theoretical massNumber of molelcules
Total (without water)108,4102
Polymers108,4102
Non-polymers00
Water36020
1
A: Protein disulfide-isomerase


Theoretical massNumber of molelcules
Total (without water)54,2051
Polymers54,2051
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Protein disulfide-isomerase


Theoretical massNumber of molelcules
Total (without water)54,2051
Polymers54,2051
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)160.748, 34.014, 156.959
Angle α, β, γ (deg.)90.00, 104.89, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Protein disulfide-isomerase / / PDI / Cellular thyroid hormone-binding protein / Prolyl 4-hydroxylase subunit beta / p55


Mass: 54204.883 Da / Num. of mol.: 2 / Fragment: oxidized full-length hPDI, UNP residues 18-479
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: P4HB, ERBA2L, PDI, PDIA1, PO4DB / Plasmid: modified pET32a / Production host: Escherichia coli (E. coli) / Strain (production host): Codon plus / References: UniProt: P07237, protein disulfide-isomerase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 20 / 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: 1.91 Å3/Da / Density % sol: 35.69 %
Crystal growTemperature: 294 K / Method: evaporation / pH: 9.8
Details: 25% PEG 3350, 0.1M Bis-Tris, 0.2M ammonium acetate, pH 9.8, EVAPORATION, temperature 294K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.979 Å
DetectorType: APEX II CCD / Detector: CCD / Date: Nov 2, 2011 / Details: MIRRORS
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.883→30 Å / Num. all: 19160 / Num. obs: 19053 / % possible obs: 99.4 % / Redundancy: 3.9 % / Biso Wilson estimate: 45.3 Å2
Reflection shell
Resolution (Å)Redundancy (%)Diffraction-ID
2.9-33.81
3-3.123.91
3.12-3.273.81

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASESphasing
PHENIX(phenix.refine: 1.7.3_928)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4EKZ

4ekz


Resolution: 2.883→29.837 Å / Occupancy max: 1 / Occupancy min: 0 / FOM work R set: 0.6946 / SU ML: 0.24 / σ(F): 1.34 / Phase error: 34.8 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2815 980 5.14 %RANDOM
Rwork0.2611 ---
obs0.2623 18223 98.91 %-
all-19160 --
Solvent computationShrinkage radii: 0.73 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 18.549 Å2 / ksol: 0.323 e/Å3
Displacement parametersBiso max: 163.54 Å2 / Biso mean: 51.9688 Å2 / Biso min: 11.12 Å2
Baniso -1Baniso -2Baniso -3
1-1.5534 Å2-0 Å21.5238 Å2
2---4.0012 Å2-0 Å2
3---2.4478 Å2
Refinement stepCycle: LAST / Resolution: 2.883→29.837 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7190 0 0 20 7210
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0157376
X-RAY DIFFRACTIONf_angle_d0.9819960
X-RAY DIFFRACTIONf_chiral_restr0.0691076
X-RAY DIFFRACTIONf_plane_restr0.0071298
X-RAY DIFFRACTIONf_dihedral_angle_d15.4342722
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 7

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.8827-3.03450.35871400.33682436257695
3.0345-3.22440.31211490.315425362685100
3.2244-3.4730.30191310.279225932724100
3.473-3.82190.30551440.26925982742100
3.8219-4.37350.24711370.230726012738100
4.3735-5.50440.2391210.230226542775100
5.5044-29.83890.27211580.24722655281397
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)
11.95450.7112-0.53682.1597-0.25871.2321-0.16380.1287-0.0723-0.2713-0.0046-0.09150.01830.12550.09190.1852-0.2216-0.00280.17470.15220.076725.2292-11.005350.0521
20.9322-0.68110.87172.1431-0.77223.63950.00090.09880.1531-0.55580.0449-0.2161-0.3572-0.1660.00260.2892-0.20950.05070.2634-0.04010.1611.0916-19.047527.7994
30.3676-0.0885-0.01631.7112-1.07983.58340.0013-0.03-0.0263-0.06680.01620.05290.2267-0.0393-0.0210.3828-0.21170.02730.68350.10980.044525.34474.5635-3.2268
41.05780.4479-0.21461.3728-0.30570.6828-0.0074-0.1057-0.08040.1029-0.1030.02660.0576-0.0417-0.01980.2562-0.4097-0.03380.33270.17180.137532.55696.931626.4271
52.6050.82621.20042.59370.75082.6852-0.0558-0.04310.0527-0.16390.1986-0.10090.1516-0.1888-0.11510.2407-0.2147-0.04050.501-0.06340.250958.5004-10.732931.8928
60.8722-0.5943-0.38291.50761.4862.1707-0.07560.2413-0.009-0.0054-0.06740.059-0.1122-0.11730.09320.3805-0.2969-0.0080.3689-0.06990.220857.04396.827162.536
73.1299-0.9780.18475.2751-0.29032.9208-0.11660.1323-0.0629-0.03130.09420.10470.19190.06010.020.20880.0249-0.12050.0212-0.03040.136332.175422.469779.2299
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain A and (resseq 20:142)A20 - 142
2X-RAY DIFFRACTION2chain A and (resseq 143:348)A143 - 348
3X-RAY DIFFRACTION3chain A and (resseq 349:478)A349 - 478
4X-RAY DIFFRACTION4chain B and (resseq 20:131)B20 - 131
5X-RAY DIFFRACTION5chain B and (resseq 132:230)B132 - 230
6X-RAY DIFFRACTION6chain B and (resseq 231:367)B231 - 367
7X-RAY DIFFRACTION7chain B and (resseq 368:478)B368 - 478

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