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- PDB-3bj5: Alternative conformations of the x region of human protein disulp... -

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Basic information

Entry
Database: PDB / ID: 3bj5
TitleAlternative conformations of the x region of human protein disulphide-isomerase modulate exposure of the substrate binding b' domain
ComponentsProtein disulfide-isomerase
KeywordsISOMERASE / Thioredoxin fold / Chaperone / Endoplasmic reticulum / Membrane / Redox-active center
Function / homology
Function and homology information


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 / LDL remodeling / thiol oxidase activity / protein disulfide-isomerase / endoplasmic reticulum chaperone complex ...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 / LDL remodeling / thiol oxidase activity / protein disulfide-isomerase / endoplasmic reticulum chaperone complex / protein folding in endoplasmic reticulum / Collagen biosynthesis and modifying enzymes / Chylomicron assembly / interleukin-23-mediated signaling pathway / 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 / endoplasmic reticulum-Golgi intermediate compartment / protein-disulfide reductase activity / endoplasmic reticulum to Golgi vesicle-mediated transport / positive regulation of substrate adhesion-dependent cell spreading / response to endoplasmic reticulum stress / positive regulation of cell adhesion / 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: 2.2 Å
AuthorsRuddock, L.W. / Nguyen, V.D. / Wierenga, R.K. / Haapalainen, A.M.
CitationJournal: J.Mol.Biol. / Year: 2008
Title: Alternative conformations of the x region of human protein disulphide-isomerase modulate exposure of the substrate binding b' domain
Authors: Nguyen, V.D. / Wallis, K. / Howard, M.J. / Haapalainen, A.M. / Salo, K.E.H. / Saaranen, M.J. / Sidhu, A. / Wierenga, R.K. / Freedman, R.B. / Ruddock, L.W. / Williamson, R.A.
History
DepositionDec 3, 2007Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 30, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Nov 10, 2021Group: Data collection / Database references / Derived calculations
Category: database_2 / diffrn_source ...database_2 / diffrn_source / 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 / _diffrn_source.pdbx_synchrotron_site / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Protein disulfide-isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,3672
Polymers17,2711
Non-polymers961
Water81145
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)57.370, 57.370, 68.310
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

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


Mass: 17270.775 Da / Num. of mol.: 1 / Fragment: b'x domain, UNPR residues 230-368 / Mutation: I272A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: P4HB, ERBA2L, PDI, PDIA1, PO4DB / Plasmid: pet23a(+) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)plysS / References: UniProt: P07237, protein disulfide-isomerase
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 45 / 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: 1.88 Å3/Da / Density % sol: 34.54 %
Crystal growTemperature: 295.15 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 2.95M Ammonium sulfate, 0.2M NaCl, 0.1M Tris-HCl pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 295.15K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X12 / Wavelength: 0.89997 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 14, 2006
RadiationMonochromator: Double crystal Si[111], horizontally focussing
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.89997 Å / Relative weight: 1
ReflectionResolution: 2.2→49.69 Å / Num. all: 6879 / Num. obs: 6879 / % possible obs: 99.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.3 % / Biso Wilson estimate: 41.042 Å2 / Rmerge(I) obs: 0.055 / Net I/σ(I): 17.84
Reflection shellResolution: 2.2→2.26 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.17 / Mean I/σ(I) obs: 17.8 / Num. unique all: 849 / % possible all: 99.3

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Processing

Software
NameVersionClassification
REFMAC5.3.0028refinement
HKL-2000data collection
XDSdata reduction
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→18.11 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.922 / SU B: 13.505 / SU ML: 0.174 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.318 / ESU R Free: 0.236 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25525 344 5 %RANDOM
Rwork0.1938 ---
obs0.19683 6533 99.29 %-
all-0 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 37.401 Å2
Baniso -1Baniso -2Baniso -3
1--0.18 Å2-0.09 Å20 Å2
2---0.18 Å20 Å2
3---0.27 Å2
Refinement stepCycle: LAST / Resolution: 2.2→18.11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1063 0 5 45 1113
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0221091
X-RAY DIFFRACTIONr_angle_refined_deg1.3621.9811468
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8825129
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.4572552
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.10115208
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.74154
X-RAY DIFFRACTIONr_chiral_restr0.0870.2160
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02807
X-RAY DIFFRACTIONr_nbd_refined0.2210.2474
X-RAY DIFFRACTIONr_nbtor_refined0.310.2722
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.190.246
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2330.236
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.240.210
X-RAY DIFFRACTIONr_mcbond_it0.7541.5674
X-RAY DIFFRACTIONr_mcangle_it1.28621053
X-RAY DIFFRACTIONr_scbond_it1.763468
X-RAY DIFFRACTIONr_scangle_it2.8414.5415
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.275 24 -
Rwork0.195 467 -
obs--99.8 %
Refinement TLS params.Method: refined / Origin x: 18.474 Å / Origin y: 3.673 Å / Origin z: 5.687 Å
111213212223313233
T-0.0834 Å2-0.0156 Å2-0.0598 Å2--0.147 Å20.0017 Å2---0.1201 Å2
L3.3596 °2-1.5443 °21.325 °2-4.2428 °20.783 °2--2.7994 °2
S0.1516 Å °-0.0463 Å °-0.1538 Å °0.1076 Å °0.0076 Å °-0.1302 Å °0.2855 Å °-0.1009 Å °-0.1592 Å °

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