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- PDB-8cpq: Crystal structure of human protein disulfide isomerase PDIA6 domain b -

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Basic information

Entry
Database: PDB / ID: 8cpq
TitleCrystal structure of human protein disulfide isomerase PDIA6 domain b
ComponentsProtein disulfide-isomerase A6
KeywordsCHAPERONE / disulfide / isomerase / endoplasmatic reticulum
Function / homology
Function and homology information


protein disulfide-isomerase / endoplasmic reticulum chaperone complex / XBP1(S) activates chaperone genes / protein disulfide isomerase activity / endoplasmic reticulum-Golgi intermediate compartment / protein-disulfide reductase activity / response to endoplasmic reticulum stress / Post-translational protein phosphorylation / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / melanosome ...protein disulfide-isomerase / endoplasmic reticulum chaperone complex / XBP1(S) activates chaperone genes / protein disulfide isomerase activity / endoplasmic reticulum-Golgi intermediate compartment / protein-disulfide reductase activity / response to endoplasmic reticulum stress / Post-translational protein phosphorylation / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / melanosome / protein folding / endoplasmic reticulum lumen / endoplasmic reticulum membrane / endoplasmic reticulum / extracellular space / extracellular exosome / plasma membrane / cytosol
Similarity search - Function
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
Protein disulfide-isomerase A6
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsJakob, R.P. / Leder, A.L. / Hiller, S. / Maier, T.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Crystal structure of human protein disulfide isomerase PDIA6 domain b
Authors: Leder, A.L. / Jakob, R.P. / Maier, T. / Hiller, S.
History
DepositionMar 3, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 13, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Protein disulfide-isomerase A6


Theoretical massNumber of molelcules
Total (without water)19,1951
Polymers19,1951
Non-polymers00
Water2,756153
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area8590 Å2
Unit cell
Length a, b, c (Å)57.384, 96.855, 63.321
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Protein disulfide-isomerase A6 / Endoplasmic reticulum protein 5 / ER protein 5 / ERp5 / Protein disulfide isomerase P5 / ...Endoplasmic reticulum protein 5 / ER protein 5 / ERp5 / Protein disulfide isomerase P5 / Thioredoxin domain-containing protein 7


Mass: 19194.660 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PDIA6, ERP5, P5, TXNDC7 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q15084, protein disulfide-isomerase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 153 / 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: 2.29 Å3/Da / Density % sol: 46.33 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 1.9M (NH4)2SO4, 0.1M Hepes 7.0, 1% DMSO

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1.00003 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Sep 7, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00003 Å / Relative weight: 1
ReflectionResolution: 1.8→49.37 Å / Num. obs: 16704 / % possible obs: 99.91 % / Redundancy: 10.2 % / CC1/2: 0.998 / CC star: 0.999 / Rmerge(I) obs: 0.1926 / Rpim(I) all: 0.0624 / Rrim(I) all: 0.2027 / Net I/σ(I): 10.5
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 10 % / Rmerge(I) obs: 1.893 / Mean I/σ(I) obs: 1.4 / Num. unique obs: 1638 / CC1/2: 0.637 / CC star: 0.882 / Rpim(I) all: 0.6231 / Rrim(I) all: 1.995 / % possible all: 99.8

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Processing

Software
NameVersionClassification
PHENIX1.12refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→49.37 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.85 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2115 867 5.19 %
Rwork0.1759 --
obs0.1779 16704 99.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.8→49.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1163 0 0 154 1317
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0041200
X-RAY DIFFRACTIONf_angle_d0.7211626
X-RAY DIFFRACTIONf_dihedral_angle_d17.569716
X-RAY DIFFRACTIONf_chiral_restr0.044172
X-RAY DIFFRACTIONf_plane_restr0.003211
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.91280.34061310.26222578X-RAY DIFFRACTION100
1.9128-2.06050.26121120.20822656X-RAY DIFFRACTION100
2.0605-2.26780.23251550.17582597X-RAY DIFFRACTION100
2.2678-2.5960.20641460.16062619X-RAY DIFFRACTION100
2.596-3.27060.21881460.16432650X-RAY DIFFRACTION100
3.2706-49.370.1811770.16662737X-RAY DIFFRACTION100
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)
11.73390.93730.67480.68690.63582.2450.04730.37920.5315-0.0734-0.01910.0011-0.0013-0.6389-0.04720.18310.01980.0570.36180.0760.2458-26.5623-20.2638-6.0227
21.29910.03730.24611.6795-0.91753.3788-0.08850.19480.0434-0.14290.08680.0422-0.0534-0.11850.0460.1498-0.01710.01210.2119-0.00810.1665-15.3968-22.9537-5.0275
31.5391-1.04560.87083.4902-2.51562.666-0.1116-0.23690.06350.19790.19920.1069-0.1514-0.3139-0.07350.17140.01350.00460.22510.00280.1986-21.9194-23.712610.0694
41.0780.061-0.41680.7921-0.43591.33810.003-0.05180.07280.00730.03130.0663-0.1433-0.0101-0.02830.1729-0.0051-0.00620.1839-0.0080.1634-11.4938-20.39620.0473
53.7109-0.6425-0.29842.7466-1.36622.96930.0398-0.19330.30260.10070.00020.1121-0.69520.11860.00420.3753-0.014-0.00920.252-0.0470.241-14.5975-11.12258.3147
64.9117-1.95320.05771.1635-0.27590.2001-0.0682-0.43520.59790.08910.1016-0.4692-0.56030.0657-0.11430.32960.0122-0.01590.3-0.07910.2848-6.7814-8.6667-0.8588
72.99180.4277-1.56090.858-0.16042.5998-0.20470.0792-0.3844-0.14780.0295-0.0920.5567-0.02610.15820.23380.0115-0.00790.1764-0.01190.2261-15.2069-34.22961.1318
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 17 through 30 )
2X-RAY DIFFRACTION2chain 'A' and (resid 31 through 51 )
3X-RAY DIFFRACTION3chain 'A' and (resid 52 through 73 )
4X-RAY DIFFRACTION4chain 'A' and (resid 74 through 118 )
5X-RAY DIFFRACTION5chain 'A' and (resid 119 through 136 )
6X-RAY DIFFRACTION6chain 'A' and (resid 137 through 145 )
7X-RAY DIFFRACTION7chain 'A' and (resid 146 through 166 )

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