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- PDB-3vww: Crystal structure of a0-domain of P5 from H. sapiens -

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Basic information

Entry
Database: PDB / ID: 3vww
TitleCrystal structure of a0-domain of P5 from H. sapiens
ComponentsProtein disulfide-isomerase A6
KeywordsISOMERASE / PDI family member / thioredoxin fold / protein disulfide isomerase
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 / Glutaredoxin / Glutaredoxin / Thioredoxin-like superfamily ...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
PHOSPHATE ION / Protein disulfide-isomerase A6
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.93 Å
AuthorsInaba, K. / Suzuki, M.
CitationJournal: Sci Rep / Year: 2013
Title: Synergistic cooperation of PDI family members in peroxiredoxin 4-driven oxidative protein folding
Authors: Sato, Y. / Kojima, R. / Okumura, M. / Hagiwara, M. / Masui, S. / Maegawa, K. / Saiki, M. / Horibe, T. / Suzuki, M. / Inaba, K.
History
DepositionSep 3, 2012Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 4, 2013Provider: 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
B: Protein disulfide-isomerase A6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,9014
Polymers25,7112
Non-polymers1902
Water3,171176
1
A: Protein disulfide-isomerase A6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,9502
Polymers12,8551
Non-polymers951
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Protein disulfide-isomerase A6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,9502
Polymers12,8551
Non-polymers951
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1620 Å2
ΔGint-9 kcal/mol
Surface area11660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.461, 43.241, 61.245
Angle α, β, γ (deg.)90.00, 101.29, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-321-

HOH

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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: 12855.474 Da / Num. of mol.: 2 / Fragment: a0 domain, UNP residues 25-140
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PDIA6, ERP5, P5, TXNDC7 / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q15084, protein disulfide-isomerase
#2: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 176 / 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: 2.28 Å3/Da / Density % sol: 46.15 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 6.7
Details: 5% PEG 4000, 50mM sodium phosphate (pH 6.7), VAPOR DIFFUSION, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Jan 21, 2010
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.93→30.03 Å / Num. obs: 17678 / % possible obs: 99.8 % / Redundancy: 3.7 % / Biso Wilson estimate: 17.58 Å2
Reflection shellResolution: 1.93→2.05 Å / Redundancy: 3.7 % / % possible all: 100

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Processing

Software
NameVersionClassification
BSSdata collection
PHASERphasing
PHENIX(phenix.refine: 1.7.3_928)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.93→30.03 Å / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.8489 / SU ML: 0.24 / σ(F): 1.35 / Phase error: 22.28 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2317 901 5.1 %random
Rwork0.1728 ---
obs0.1757 17672 99.78 %-
Solvent computationShrinkage radii: 0.6 Å / VDW probe radii: 0.9 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 36.489 Å2 / ksol: 0.364 e/Å3
Displacement parametersBiso max: 85.44 Å2 / Biso mean: 22.1354 Å2 / Biso min: 6.11 Å2
Baniso -1Baniso -2Baniso -3
1--0.9428 Å20 Å2-4.1542 Å2
2---1.5458 Å2-0 Å2
3---2.4887 Å2
Refinement stepCycle: LAST / Resolution: 1.93→30.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1812 0 10 176 1998
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061868
X-RAY DIFFRACTIONf_angle_d1.0282536
X-RAY DIFFRACTIONf_dihedral_angle_d12.599680
X-RAY DIFFRACTIONf_chiral_restr0.075274
X-RAY DIFFRACTIONf_plane_restr0.004330
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 6

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.9285-2.04930.27781630.19172743100
2.0493-2.20750.24991480.17122775100
2.2075-2.42960.23181400.16892785100
2.4296-2.78090.28831460.18252821100
2.7809-3.50280.19671540.17122784100
3.5028-30.0340.21331500.1668286399
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)
18.88032.00335.50464.80263.78355.4104-0.00730.03830.2321-0.3558-0.0333-0.37210.08350.36790.0550.18020.01070.06960.10840.0230.187438.435340.2741-2.0805
24.927-0.1533-0.61134.47380.08855.86710.08640.3624-0.6224-0.6298-0.0844-0.52190.82680.72150.06860.10380.02550.08540.161-0.07230.169236.908429.5862-0.1069
32.6473-4.63091.08679.84-3.1971.5375-0.02620.09180.05710.07660.1311-0.1178-0.14650.0562-0.08080.1038-0.0453-0.00580.0955-0.00970.108530.269144.72741.8294
44.6753-2.58871.94993.6698-2.18843.6411-0.2725-0.02180.30130.14850.1818-0.5279-0.55450.26250.02250.0442-0.01290.03230.1108-0.0590.164237.09545.96859.5123
53.6568-0.40771.51773.82490.40613.99630.13350.4817-0.287-0.4262-0.17660.26370.0769-0.14750.06160.1133-0.00030.020.0188-0.03990.142729.462941.1283-3.8772
60.03450.3721-0.03415.67250.26491.4373-0.05920.0076-0.0286-0.04070.06070.5632-0.0411-0.0389-0.02740.0841-0.00780.02180.0932-0.00590.138126.2736.5764.1078
78.6663-1.9231.47692.40821.67592.2930.1449-0.0989-0.61220.2801-0.1312-0.00210.4304-0.4582-0.07850.1808-0.02010.02920.1455-0.00950.185625.00530.24876.5742
84.4863-3.7823-0.56793.59320.73272.201-0.0583-0.1939-0.10130.30430.11360.32560.04260.025-0.11080.06540.0135-0.00860.1352-0.01390.108332.943733.735916.0001
92.9055-3.08720.2764.30880.82681.40780.4470.7050.5935-0.8586-0.5619-0.7158-0.03030.0762-0.07870.15710.03230.03540.1458-0.00180.031358.34526.80714.9602
103.1713-1.00350.65853.6073-0.52022.02830.0954-0.0386-0.1870.1113-0.0504-0.00390.1274-0.0011-0.03390.08130.00630.0130.0648-0.00310.047855.503719.921123.0429
115.80154.3027-1.38255.3579-1.4424.12760.2192-0.76530.43750.4479-0.38290.4493-0.1747-0.12970.10370.17450.0270.03830.2644-0.03560.118651.039626.033829.7084
122.2695-1.58510.3834.6427-2.74573.0651-0.1259-0.25820.22150.62790.1070.7094-0.3041-0.2127-0.02820.09490.03270.00060.1311-0.04050.157842.706632.512722.5723
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resseq 27:36)A27 - 36
2X-RAY DIFFRACTION2chain 'A' and (resseq 37:47)A37 - 47
3X-RAY DIFFRACTION3chain 'A' and (resseq 48:57)A48 - 57
4X-RAY DIFFRACTION4chain 'A' and (resseq 58:78)A58 - 78
5X-RAY DIFFRACTION5chain 'A' and (resseq 79:94)A79 - 94
6X-RAY DIFFRACTION6chain 'A' and (resseq 95:110)A95 - 110
7X-RAY DIFFRACTION7chain 'A' and (resseq 111:115)A111 - 115
8X-RAY DIFFRACTION8chain 'A' and (resseq 116:142)A116 - 142
9X-RAY DIFFRACTION9chain 'B' and (resseq 27:47)B27 - 47
10X-RAY DIFFRACTION10chain 'B' and (resseq 48:110)B48 - 110
11X-RAY DIFFRACTION11chain 'B' and (resseq 111:121)B111 - 121
12X-RAY DIFFRACTION12chain 'B' and (resseq 122:142)B122 - 142

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