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- PDB-5gu6: Crystal structure of Human ERp44 form I -

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Basic information

Entry
Database: PDB / ID: 5gu6
TitleCrystal structure of Human ERp44 form I
ComponentsEndoplasmic reticulum resident protein 44
KeywordsCHAPERONE / quality control
Function / homology
Function and homology information


glycoprotein metabolic process / protein disulfide isomerase activity / endoplasmic reticulum-Golgi intermediate compartment / response to unfolded protein / response to endoplasmic reticulum stress / cell redox homeostasis / specific granule lumen / protein folding / endoplasmic reticulum lumen / Neutrophil degranulation ...glycoprotein metabolic process / protein disulfide isomerase activity / endoplasmic reticulum-Golgi intermediate compartment / response to unfolded protein / response to endoplasmic reticulum stress / cell redox homeostasis / specific granule lumen / protein folding / endoplasmic reticulum lumen / Neutrophil degranulation / endoplasmic reticulum membrane / cell surface / extracellular exosome / extracellular region
Similarity search - Function
Endoplasmic reticulum resident protein 44, TRX-like domain b' / Endoplasmic reticulum resident protein 44, TRX-like domain b / Thioredoxin-like domain / Endoplasmic reticulum targeting sequence. / Thioredoxin / Thioredoxin domain profile. / Thioredoxin domain / Glutaredoxin / Glutaredoxin / Thioredoxin-like superfamily ...Endoplasmic reticulum resident protein 44, TRX-like domain b' / Endoplasmic reticulum resident protein 44, TRX-like domain b / Thioredoxin-like domain / Endoplasmic reticulum targeting sequence. / Thioredoxin / Thioredoxin domain profile. / Thioredoxin domain / Glutaredoxin / Glutaredoxin / Thioredoxin-like superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Endoplasmic reticulum resident protein 44
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsWatanabe, S. / Inaba, K.
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2017
Title: Structural basis of pH-dependent client binding by ERp44, a key regulator of protein secretion at the ER-Golgi interface
Authors: Watanabe, S. / Harayama, M. / Kanemura, S. / Sitia, R. / Inaba, K.
History
DepositionAug 26, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 12, 2017Provider: repository / Type: Initial release
Revision 1.1May 3, 2017Group: 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Endoplasmic reticulum resident protein 44
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,8672
Polymers43,8311
Non-polymers351
Water2,000111
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area130 Å2
ΔGint-10 kcal/mol
Surface area19630 Å2
2
A: Endoplasmic reticulum resident protein 44
hetero molecules

A: Endoplasmic reticulum resident protein 44
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,7334
Polymers87,6622
Non-polymers712
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_554x-y,-y,-z-1/31
Buried area2890 Å2
ΔGint-29 kcal/mol
Surface area36640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.630, 81.630, 139.910
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11A-558-

HOH

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Components

#1: Protein Endoplasmic reticulum resident protein 44 / ERp44 / Thioredoxin domain-containing protein 4


Mass: 43831.191 Da / Num. of mol.: 1 / Fragment: UNP residues 30-402
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ERP44, KIAA0573, TXNDC4, UNQ532/PRO1075 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9BS26
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 111 / 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: 3.07 Å3/Da / Density % sol: 59.94 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.2 / Details: Polyethylene glycol (PEG) 8000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Apr 18, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2→19.61 Å / Num. obs: 36963 / % possible obs: 99.5 % / Redundancy: 18.2 % / CC1/2: 0.998 / Rmerge(I) obs: 0.075 / Net I/σ(I): 22.5
Reflection shellResolution: 2→2.07 Å / Redundancy: 11.14 % / Rmerge(I) obs: 1.125 / Mean I/σ(I) obs: 2.2 / CC1/2: 0.759 / % possible all: 99.12

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2R2J

2r2j


Resolution: 2→19.607 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 27.84
RfactorNum. reflection% reflection
Rfree0.2405 1782 4.82 %
Rwork0.204 --
obs0.2057 36959 99.65 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2→19.607 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3029 0 1 111 3141
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0043166
X-RAY DIFFRACTIONf_angle_d0.6654297
X-RAY DIFFRACTIONf_dihedral_angle_d18.8451187
X-RAY DIFFRACTIONf_chiral_restr0.048459
X-RAY DIFFRACTIONf_plane_restr0.006576
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.05410.33421410.30572618X-RAY DIFFRACTION99
2.0541-2.11440.28641070.27722700X-RAY DIFFRACTION100
2.1144-2.18260.32421360.26022658X-RAY DIFFRACTION100
2.1826-2.26050.29521470.25162663X-RAY DIFFRACTION100
2.2605-2.35090.31781340.25352678X-RAY DIFFRACTION100
2.3509-2.45770.26981210.24942695X-RAY DIFFRACTION100
2.4577-2.5870.25051470.24452675X-RAY DIFFRACTION100
2.587-2.74860.31051380.25512705X-RAY DIFFRACTION100
2.7486-2.96020.32051210.2552729X-RAY DIFFRACTION100
2.9602-3.25690.29851470.24992721X-RAY DIFFRACTION100
3.2569-3.72530.2621230.20512755X-RAY DIFFRACTION100
3.7253-4.6830.19771780.16192724X-RAY DIFFRACTION100
4.683-19.60780.19471420.17032856X-RAY DIFFRACTION99
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)
13.23870.4491-0.17682.9139-0.51091.97290.1408-0.4654-0.24310.7098-0.1232-0.4338-0.0280.264-0.04370.6333-0.0233-0.20890.39450.02920.4656-28.1113.59466.8707
23.5637-0.39220.3164.7412-0.97931.82360.2250.0975-0.4446-0.17060.0125-0.86670.23080.4466-0.18340.4822-0.0232-0.08440.5747-0.02650.6359-7.033622.45-3.4393
31.77010.3228-0.75651.8801-1.25983.977-0.05340.23570.32260.1527-0.1516-0.3075-0.68260.06420.17870.589-0.0259-0.15080.29390.06180.4783-31.803314.4704-25.5896
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid -4 through 112)
2X-RAY DIFFRACTION2chain 'A' and (resid 113 through 215 )
3X-RAY DIFFRACTION3chain 'A' and (resid 216 through 373 )

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