[English] 日本語
Yorodumi
- PDB-2r2j: crystal structure of human ERp44 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2r2j
Titlecrystal structure of human ERp44
ComponentsThioredoxin domain-containing protein 4
KeywordsCHAPERONE / thioredoxin / CRFS motif / Endoplasmic reticulum / Stress response
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
FORMIC ACID / SUCCINIC ACID / Endoplasmic reticulum resident protein 44
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.6 Å
AuthorsWang, L.K. / Li, S.J. / Sun, F. / Wang, C.C.
CitationJournal: Embo Rep. / Year: 2008
Title: Crystal structure of human ERp44 shows a dynamic functional modulation by its carboxy-terminal tail.
Authors: Wang, L.K. / Wang, L. / Vavassori, S. / Li, S.J. / Ke, H. / Anelli, T. / Degano, M. / Ronzoni, R. / Sitia, R. / Sun, F. / Wang, C.C.
History
DepositionAug 25, 2007Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jul 8, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Thioredoxin domain-containing protein 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,7714
Polymers44,5611
Non-polymers2103
Water1,982110
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Thioredoxin domain-containing protein 4
hetero molecules

A: Thioredoxin domain-containing protein 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,5428
Polymers89,1212
Non-polymers4206
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_765-x+2,-x+y+1,-z+1/31
Buried area2110 Å2
ΔGint-7 kcal/mol
Surface area34610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.501, 83.501, 123.137
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

-
Components

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


Mass: 44560.727 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TXNDC4, ERP44, KIAA0573 / Plasmid: pGEX-6P-1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)plysS / References: UniProt: Q9BS26
#2: Chemical ChemComp-SIN / SUCCINIC ACID


Mass: 118.088 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H6O4
#3: Chemical ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CH2O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 110 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 3.03 Å3/Da / Density % sol: 59.15 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: disodium succinate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 21, 2006
RadiationProtocol: SAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.6→72.36 Å / Num. all: 15807 / Num. obs: 15728 / % possible obs: 99.5 % / Redundancy: 6.3 % / Biso Wilson estimate: 79.2 Å2 / Rmerge(I) obs: 0.054 / Net I/σ(I): 26.7
Reflection shellResolution: 2.6→2.69 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.394 / Mean I/σ(I) obs: 2.5 / Num. unique all: 1488 / % possible all: 96.6

-
Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
SOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 2.6→72.36 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.916 / SU B: 23.033 / SU ML: 0.241 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.511 / ESU R Free: 0.304 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26302 783 5 %RANDOM
Rwork0.21694 ---
obs0.21911 14916 99.49 %-
all-15807 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 73.575 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20.01 Å20 Å2
2--0.01 Å20 Å2
3----0.02 Å2
Refinement stepCycle: LAST / Resolution: 2.6→72.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2694 0 14 110 2818
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0222778
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.9461.9523747
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9295327
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.91524.2150
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.22615486
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.3411519
X-RAY DIFFRACTIONr_chiral_restr0.130.2401
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022134
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2520.21342
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.320.21860
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2070.2137
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2610.228
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2490.26
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.8331.51677
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.91722665
X-RAY DIFFRACTIONr_scbond_it1.72331217
X-RAY DIFFRACTIONr_scangle_it2.5474.51080
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.6→2.668 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.312 65 -
Rwork0.289 1018 -
obs--95.76 %
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)
17.0816-3.4633-0.72877.93520.75594.16870.0869-1.14020.59190.6760.07760.0737-0.3144-0.0312-0.1645-0.1446-0.04380.08930.0934-0.0158-0.27651.762842.155350.8126
28.83572.43830.61386.89282.86655.58320.2026-0.04351.3835-0.12560.0253-0.2386-0.6759-0.1736-0.2279-0.14910.08750.2513-0.1982-0.02470.130326.796352.395943.8382
38.59192.1725-0.91823.9662-0.09037.0321-0.09610.23990.0526-0.36270.0310.608-0.1606-0.89920.0651-0.31470.05570.1084-0.08350.0602-0.235340.846341.821518.9572
45.7956-0.35424.10511.3169-2.47886.74020.03490.5172-0.8041-0.20520.2409-0.43060.69760.3726-0.2758-0.18720.00230.2421-0.12660.1284-0.135354.707935.170524.0074
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA3 - 508 - 55
2X-RAY DIFFRACTION1AA54 - 11259 - 117
3X-RAY DIFFRACTION2AA113 - 118118 - 123
4X-RAY DIFFRACTION2AA131 - 169136 - 174
5X-RAY DIFFRACTION2AA178 - 215183 - 220
6X-RAY DIFFRACTION3AA216 - 325221 - 330
7X-RAY DIFFRACTION4AA326 - 331331 - 336
8X-RAY DIFFRACTION4AA351 - 372356 - 377

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbjlvh1.pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more