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- PDB-8gdy: Crystal structure of the human PDI first domain with 9 mutations -

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Basic information

Entry
Database: PDB / ID: 8gdy
TitleCrystal structure of the human PDI first domain with 9 mutations
ComponentsProtein disulfide-isomerase
KeywordsISOMERASE / PDI
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 / Thioredoxin-like superfamily
Similarity search - Domain/homology
THIOCYANATE ION / Protein disulfide-isomerase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 Å
AuthorsForouhar, F. / Banayan, N.E. / Loughlin, B.L. / Singh, S. / Wong, V. / Hunt, H.S. / Handelman, S.K. / Price, N. / Hunt, J.F.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Protein Sci. / Year: 2024
Title: Systematic enhancement of protein crystallization efficiency by bulk lysine-to-arginine (KR) substitution.
Authors: Banayan, N.E. / Loughlin, B.J. / Singh, S. / Forouhar, F. / Lu, G. / Wong, K.H. / Neky, M. / Hunt, H.S. / Bateman Jr., L.B. / Tamez, A. / Handelman, S.K. / Price, W.N. / Hunt, J.F.
History
DepositionMar 6, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 24, 2024Provider: repository / Type: Initial release
Revision 1.1Mar 20, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,8415
Polymers31,6632
Non-polymers1783
Water2,558142
1
A: Protein disulfide-isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,9523
Polymers15,8321
Non-polymers1202
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Protein disulfide-isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,8902
Polymers15,8321
Non-polymers581
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)58.706, 61.303, 68.561
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 15831.599 Da / Num. of mol.: 2
Mutation: K31R, K42R, K57R, K65R, K69R, K71R, K114R, K130R, K131R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: P4HB, ERBA2L, PDI, PDIA1, PO4DB / Production host: Escherichia coli (E. coli) / References: UniProt: P07237, protein disulfide-isomerase
#2: Chemical ChemComp-SCN / THIOCYANATE ION / Thiocyanate


Mass: 58.082 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CNS / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 142 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 1.95 Å3/Da / Density % sol: 36.98 %
Crystal growTemperature: 277 K / Method: microbatch / pH: 6
Details: 0.1 M potassium thiocyanate, 0.1 M MES, and 24% (w/v) PEG 20k

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.979 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 13, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.89→68.56 Å / Num. obs: 20332 / % possible obs: 98.8 % / Redundancy: 12.8 % / CC1/2: 0.993 / Rmerge(I) obs: 0.238 / Net I/σ(I): 7
Reflection shellResolution: 1.89→1.93 Å / Redundancy: 10.4 % / Rmerge(I) obs: 2.148 / Num. unique obs: 1062 / CC1/2: 0.457 / % possible all: 82.2

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Processing

Software
NameVersionClassification
PHENIX1.17refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.05→45.7 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 32.13 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2391 1574 9.83 %
Rwork0.1924 --
obs0.1972 16013 99.59 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.05→45.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1897 0 10 142 2049
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061948
X-RAY DIFFRACTIONf_angle_d0.7952635
X-RAY DIFFRACTIONf_dihedral_angle_d35.811721
X-RAY DIFFRACTIONf_chiral_restr0.054270
X-RAY DIFFRACTIONf_plane_restr0.004356
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.05-2.120.37361420.28341286X-RAY DIFFRACTION100
2.12-2.190.271240.25031324X-RAY DIFFRACTION100
2.19-2.280.29161480.2341267X-RAY DIFFRACTION99
2.28-2.380.30071480.20351280X-RAY DIFFRACTION100
2.38-2.510.26261520.18941281X-RAY DIFFRACTION100
2.51-2.670.3041420.20541320X-RAY DIFFRACTION99
2.67-2.870.23641490.20751279X-RAY DIFFRACTION99
2.87-3.160.27491100.1931340X-RAY DIFFRACTION99
3.16-3.620.26711570.18731307X-RAY DIFFRACTION100
3.62-4.560.17761600.15751336X-RAY DIFFRACTION100
4.56-45.70.18861420.17731419X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: -15.3877 Å / Origin y: -15.1971 Å / Origin z: 16.9988 Å
111213212223313233
T0.1822 Å20.001 Å2-0.0015 Å2-0.1799 Å2-0.0073 Å2--0.1886 Å2
L0.1996 °2-0.1214 °20.0652 °2-0.3139 °2-0.2265 °2--0.1826 °2
S-0.0399 Å °-0.0012 Å °0.0149 Å °-0.0044 Å °-0.0148 Å °-0.0043 Å °-0.0417 Å °-0.0322 Å °-0 Å °
Refinement TLS groupSelection details: all

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