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- SASDH32: Protein Disulfide Isomerase (PDI) in Complex with Ribonuclease-A ... -

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ID or keywords:

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Basic information

Entry
Database: SASBDB / ID: SASDH32
SampleProtein Disulfide Isomerase (PDI) in Complex with Ribonuclease-A (RNase)
  • Protein disulfide-isomerase (protein), PDI, Bos taurus
  • Ribonuclease pancreaticPancreatic ribonuclease family (protein), RNase-A, Bos taurus
Function / homology
Function and homology information


procollagen-proline 4-dioxygenase activity / protein disulfide-isomerase / peptidyl-proline hydroxylation to 4-hydroxy-L-proline / pancreatic ribonuclease / ribonuclease A activity / protein disulfide isomerase activity / RNA nuclease activity / response to endoplasmic reticulum stress / melanosome / protein folding ...procollagen-proline 4-dioxygenase activity / protein disulfide-isomerase / peptidyl-proline hydroxylation to 4-hydroxy-L-proline / pancreatic ribonuclease / ribonuclease A activity / protein disulfide isomerase activity / RNA nuclease activity / response to endoplasmic reticulum stress / melanosome / protein folding / nucleic acid binding / lyase activity / defense response to Gram-positive bacterium / protein heterodimerization activity / external side of plasma membrane / endoplasmic reticulum lumen / endoplasmic reticulum / extracellular region
Similarity search - Function
Protein disulphide isomerase / Thioredoxin-like domain / Disulphide isomerase / Endoplasmic reticulum targeting sequence. / Thioredoxin / Pancreatic ribonuclease / Ribonuclease A, active site / Ribonuclease A-domain / Ribonuclease A-like domain superfamily / Pancreatic ribonuclease ...Protein disulphide isomerase / Thioredoxin-like domain / Disulphide isomerase / Endoplasmic reticulum targeting sequence. / Thioredoxin / Pancreatic ribonuclease / Ribonuclease A, active site / Ribonuclease A-domain / Ribonuclease A-like domain superfamily / Pancreatic ribonuclease / Pancreatic ribonuclease family signature. / Pancreatic ribonuclease / Thioredoxin, conserved site / Thioredoxin family active site. / Thioredoxin domain profile. / Thioredoxin domain / Thioredoxin-like superfamily
Similarity search - Domain/homology
Protein disulfide-isomerase / Ribonuclease pancreatic
Similarity search - Component
Biological speciesBos taurus (cattle)
Contact author
  • Chandra Sekar (Pondicherry University)

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Models

Model #3887
Type: dummy / Software: (dammif (r9988)) / Radius of dummy atoms: 2.70 A / Symmetry: P1 / Chi-square value: 1.200 / P-value: 0.094060
Model #3888
Type: dummy / Radius of dummy atoms: 2.70 A / Symmetry: P1 / Chi-square value: 1.200 / P-value: 0.094060
Model #3890
Type: dummy / Radius of dummy atoms: 2.70 A / Symmetry: P1 / Chi-square value: 1.203 / P-value: 0.094060
Model #3891
Type: dummy / Software: (dammif (r9988)) / Radius of dummy atoms: 2.70 A / Symmetry: P1 / Chi-square value: 1.203 / P-value: 0.094060
Model #3892
Type: dummy / Software: (DAMFILT 5.0 (r9988)) / Radius of dummy atoms: 2.75 A / Symmetry: P1 / Chi-square value: 1.206 / P-value: 0.094060

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Sample

SampleName: Protein Disulfide Isomerase (PDI) in Complex with Ribonuclease-A (RNase)
Specimen concentration: 2.50-10.00 / Entity id: 1946 / 1947
BufferName: 50 mM Tris-HCL, 150 mM NaCl / pH: 7.5
Comment: PDI was incubated with 0.5mM TCEP to reduce the Active sites one hour before SAXS data collection
Entity #1946Name: PDI / Type: protein / Description: Protein disulfide-isomerase / Formula weight: 57.265 / Num. of mol.: 1 / Source: Bos taurus / References: UniProt: P05307
Sequence: MLRRALLCLA LTALFRAGAG APDEEDHVLV LHKGNFDEAL AAHKYLLVEF YAPWCGHCKA LAPEYAKAAG KLKAEGSEIR LAKVDATEES DLAQQYGVRG YPTIKFFKNG DTASPKEYTA GREADDIVNW LKKRTGPAAS TLSDGAAAEA LVESSEVAVI GFFKDMESDS ...Sequence:
MLRRALLCLA LTALFRAGAG APDEEDHVLV LHKGNFDEAL AAHKYLLVEF YAPWCGHCKA LAPEYAKAAG KLKAEGSEIR LAKVDATEES DLAQQYGVRG YPTIKFFKNG DTASPKEYTA GREADDIVNW LKKRTGPAAS TLSDGAAAEA LVESSEVAVI GFFKDMESDS AKQFFLAAEV IDDIPFGITS NSDVFSKYQL DKDGVVLFKK FDEGRNNFEG EVTKEKLLDF IKHNQLPLVI EFTEQTAPKI FGGEIKTHIL LFLPKSVSDY EGKLSNFKKA AESFKGKILF IFIDSDHTDN QRILEFFGLK KEECPAVRLI TLEEEMTKYK PESDELTAEK ITEFCHRFLE GKIKPHLMSQ ELPDDWDKQP VKVLVGKNFE EVAFDEKKNV FVEFYAPWCG HCKQLAPIWD KLGETYKDHE NIVIAKMDST ANEVEAVKVH SFPTLKFFPA SADRTVIDYN GERTLDGFKK FLESGGQDGA GDDDDLEDLE EAEEPDLEED DDQKAVKDEL
Entity #1947Name: RNase-A / Type: protein
Description: Ribonuclease pancreaticPancreatic ribonuclease family
Formula weight: 13.69 / Num. of mol.: 1 / Source: Bos taurus / References: UniProt: P61823
Sequence:
KETAAAKFER QHMDSSTSAA SSSNYCNQMM KSRNLTKDRC KPVNTFVHES LADVQAVCSQ KNVACKNGQT NCYQSYSTMS ITDCRETGSS KYPNCAYKTT QANKHIIVAC EGNPYVPVHF DASV

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Experimental information

BeamInstrument name: Advanced Photon Source (APS), Argonne National Laboratory BioCAT 18ID
City: Lemont, IL / 国: USA / Type of source: X-ray synchrotronSynchrotron / Wavelength: 0.1033 Å / Dist. spec. to detc.: 3.485 mm
DetectorName: Pilatus3 X 1M / Pixsize x: 0.172 mm
Scan
Title: Protein Disulfide Isomerase (PDI) in Complex with Ribonuclease-A (RNase)
Measurement date: Nov 4, 2015 / Storage temperature: 10 °C / Cell temperature: 10 °C / Exposure time: 1 sec. / Number of frames: 8 / Unit: 1/A /
MinMax
Q0.0243 0.392
Distance distribution function P(R)
Sofotware P(R): GNOM 5.0 / Number of points: 819 /
MinMax
Q0.0242822 0.268798
P(R) point1 819
R0 90.78
Result
Type of curve: merged
Comments: PDI was purified from bovine liver. Ribonuclease A (Type III-A) was purchased from SIGMA-ALDRICH in the form of lyophilized powder, dissolved with suspension medium and used directly ...Comments: PDI was purified from bovine liver. Ribonuclease A (Type III-A) was purchased from SIGMA-ALDRICH in the form of lyophilized powder, dissolved with suspension medium and used directly without any further purification. RNase was mixed with PDI just before to SAXS data collection. CAUTION! The quoted experimental MW from I(0) = 56 kDa; From Bayesian inference = 44 kDa; From Porod volume = 53 kDa. The expected MW of a fully-formed 1:1 complex is 71 kDa, calculated from the amino acid sequence. Therefore, the data likely represent a mixture of components and not a complex.
ExperimentalStandardPorod
MW70.956 kDa56.826 kDa53 kDa
Volume--85 nm3

P(R)GuinierGuinier error
Forward scattering, I029.2 29.83 0.15
Radius of gyration, Rg2.9 nm2.97 nm0.04

MinMax
D-9.08
Guinier point1 65

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