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- PDB-4ekz: Crystal structure of reduced hPDI (abb'xa') -

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Basic information

Entry
Database: PDB / ID: 4ekz
TitleCrystal structure of reduced hPDI (abb'xa')
ComponentsProtein disulfide-isomerase
KeywordsCHAPERONE / abb'a' domains / "CGHC" active sites / Horseshoe shape / An 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: 2.51 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


Theoretical massNumber of molelcules
Total (without water)54,2051
Polymers54,2051
Non-polymers00
Water1,56787
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)38.453, 100.586, 123.767
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: 54204.883 Da / Num. of mol.: 1 / Fragment: reduced 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.: 87 / 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: 2.21 Å3/Da / Density % sol: 44.29 %
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: Oct 3, 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: 2.5→30 Å / Num. all: 17068 / Num. obs: 16370 / % possible obs: 95.9 % / Redundancy: 3.1 % / Biso Wilson estimate: 39.53 Å2
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 3.1 % / Num. unique all: 17068

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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: PDB ENTRY 3UEM

3uem


Resolution: 2.51→29.574 Å / Occupancy max: 1 / Occupancy min: 0 / FOM work R set: 0.8166 / SU ML: 0.31 / σ(F): 1.33 / Phase error: 24.69 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2502 1634 10.01 %RANDOM
Rwork0.2361 ---
obs0.2375 16316 95.25 %-
all-17068 --
Solvent computationShrinkage radii: 0.98 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 23.898 Å2 / ksol: 0.294 e/Å3
Displacement parametersBiso max: 193.17 Å2 / Biso mean: 47.0292 Å2 / Biso min: 16.07 Å2
Baniso -1Baniso -2Baniso -3
1-2.0177 Å20 Å2-0 Å2
2--2.2692 Å20 Å2
3----4.2869 Å2
Refinement stepCycle: LAST / Resolution: 2.51→29.574 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3712 0 0 87 3799
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.013798
X-RAY DIFFRACTIONf_angle_d1.2175126
X-RAY DIFFRACTIONf_chiral_restr0.089551
X-RAY DIFFRACTIONf_plane_restr0.009669
X-RAY DIFFRACTIONf_dihedral_angle_d17.9261399
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 12

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.5099-2.58370.28871250.33071115124088
2.5837-2.6670.33991350.31341214134998
2.667-2.76230.35761410.30691258139998
2.7623-2.87280.26821340.29461210134497
2.8728-3.00340.29231370.28771236137397
3.0034-3.16160.26791390.2711241138097
3.1616-3.35940.27511350.25061213134897
3.3594-3.61840.2771370.23771242137997
3.6184-3.98170.21081370.221221135896
3.9817-4.55610.19091360.17861233136995
4.5561-5.73330.221370.20551232136994
5.7333-29.57620.24491410.2091267140890
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)
14.84320.12570.04244.74221.61763.5360.06910.046-0.0077-0.0693-0.04830.1081-0.16350.0043-0.02380.11680.01090.02370.10710.00580.1343-2.3138-15.14466.8678
23.95330.5738-0.00974.2519-0.26033.08060.13440.2626-0.3019-0.451-0.04340.09570.2865-0.151-0.03140.31330.0333-0.04430.20450.04030.186413.6315-30.516428.5504
34.5552-0.92710.93365.6017-0.03187.70380.21430.04160.10530.0096-0.34110.1208-0.1481-0.73890.17560.2286-0.0229-0.02860.3662-0.0140.2584-3.1093-56.310623.4753
41.9143-0.7501-0.12672.86920.77172.5307-0.0426-0.2045-0.07990.15210.06620.07720.2336-0.11210.0023-0.0502-0.03140.0055-0.0023-0.01-0.0359-6.5321-61.1472-6.5136
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1CHAIN A AND (RESSEQ 18:132)A18 - 132
2X-RAY DIFFRACTION2CHAIN A AND (RESSEQ 133:254)A133 - 254
3X-RAY DIFFRACTION3CHAIN A AND (RESSEQ 255:347)A255 - 347
4X-RAY DIFFRACTION4CHAIN A AND (RESSEQ 348:478)A348 - 478

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