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- PDB-5gu7: Crystal Structure of human ERp44 form II -

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Basic information

Entry
Database: PDB / ID: 5gu7
TitleCrystal Structure of human ERp44 form II
ComponentsEndoplasmic reticulum resident protein 44
KeywordsCHAPERONE / quality control
Function / homology
Function and homology information


glycoprotein metabolic process / protein disulfide isomerase activity / response to unfolded protein / endoplasmic reticulum-Golgi intermediate compartment / 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 / response to unfolded protein / endoplasmic reticulum-Golgi intermediate compartment / 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: 2.05 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

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Assembly

Deposited unit
C: Endoplasmic reticulum resident protein 44


Theoretical massNumber of molelcules
Total (without water)45,7201
Polymers45,7201
Non-polymers00
Water2,630146
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area19150 Å2
2
C: Endoplasmic reticulum resident protein 44

C: Endoplasmic reticulum resident protein 44


Theoretical massNumber of molelcules
Total (without water)91,4412
Polymers91,4412
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
Buried area2400 Å2
ΔGint-15 kcal/mol
Surface area35900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.150, 84.150, 133.180
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 Endoplasmic reticulum resident protein 44 / ERp44 / Thioredoxin domain-containing protein 4


Mass: 45720.273 Da / Num. of mol.: 1
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: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 146 / 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: 2.98 Å3/Da / Density % sol: 58.69 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: Na/K tartrate

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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: 2.05→37.913 Å / Num. obs: 34847 / % possible obs: 99.9 % / Redundancy: 17.1 % / CC1/2: 0.999 / Rmerge(I) obs: 0.063 / Net I/σ(I): 26
Reflection shellResolution: 2.05→2.1 Å / Redundancy: 11.24 % / Rmerge(I) obs: 1.176 / Mean I/σ(I) obs: 2.3 / CC1/2: 0.764 / % possible all: 100

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Processing

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

2r2j


Resolution: 2.05→37.913 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.89
RfactorNum. reflection% reflection
Rfree0.2354 1713 4.92 %
Rwork0.1999 --
obs0.2017 34844 99.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.05→37.913 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2966 0 0 146 3112
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073080
X-RAY DIFFRACTIONf_angle_d0.8524170
X-RAY DIFFRACTIONf_dihedral_angle_d18.8661154
X-RAY DIFFRACTIONf_chiral_restr0.06445
X-RAY DIFFRACTIONf_plane_restr0.006553
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0501-2.11040.30691420.26872705X-RAY DIFFRACTION100
2.1104-2.17860.27971190.25422734X-RAY DIFFRACTION100
2.1786-2.25640.26691490.24342730X-RAY DIFFRACTION100
2.2564-2.34670.25641500.23132710X-RAY DIFFRACTION100
2.3467-2.45350.30331420.22912723X-RAY DIFFRACTION100
2.4535-2.58290.24081340.23142747X-RAY DIFFRACTION100
2.5829-2.74460.29271550.24462729X-RAY DIFFRACTION100
2.7446-2.95650.31511380.25032760X-RAY DIFFRACTION100
2.9565-3.25380.31251350.23772780X-RAY DIFFRACTION100
3.2538-3.72430.21191320.19242796X-RAY DIFFRACTION100
3.7243-4.69090.1881630.15812798X-RAY DIFFRACTION100
4.6909-37.91930.21441540.17922919X-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)
13.21360.37460.14421.29610.02831.27390.08080.75990.169-0.06470.00550.0566-0.1582-0.07130.00040.36720.09210.01290.62660.01620.3823-12.6626-29.0429-30.7167
21.2941-0.62090.15511.0002-0.92441.02140.04270.01570.55950.08440.1502-0.0582-0.22120.16860.00660.4354-0.07490.11780.4667-0.05530.599814.4535-18.1849-21.254
32.0194-0.1674-0.51160.88420.64591.8654-0.111-0.19-0.16390.09630.02670.0002-0.02190.2357-0.00120.33740.05250.03660.44390.01160.3683-3.731-34.60520.7486
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'C' and (resid -9 through 112)
2X-RAY DIFFRACTION2chain 'C' and (resid 113 through 215 )
3X-RAY DIFFRACTION3chain 'C' and (resid 216 through 373 )

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