[English] 日本語
Yorodumi
- PDB-2hj3: Structure of the Arabidopsis Thaliana Erv1 Thiol Oxidase -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2hj3
TitleStructure of the Arabidopsis Thaliana Erv1 Thiol Oxidase
ComponentsSulfhydryl oxidase Erv1p
KeywordsOXIDOREDUCTASE / four-helix bundle / flavin adenine dinucleotide
Function / homology
Function and homology information


flavin-dependent sulfhydryl oxidase activity / thiol oxidase / thiol oxidase activity / protein-disulfide reductase activity / flavin adenine dinucleotide binding / mitochondrion / identical protein binding
Similarity search - Function
Sulfhydryl oxidase ALR/ERV / ERV/ALR sulfhydryl oxidase domain / ERV/ALR sulfhydryl oxidase domain / ERV/ALR sulfhydryl oxidase domain superfamily / Erv1 / Alr family / ERV/ALR sulfhydryl oxidase domain profile. / Four Helix Bundle (Hemerythrin (Met), subunit A) / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / FAD-linked sulfhydryl oxidase ERV1 / FAD-linked sulfhydryl oxidase ERV1
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.5 Å
AuthorsVitu, E. / Fass, D.
CitationJournal: J.Mol.Biol. / Year: 2006
Title: Gain of Function in an ERV/ALR Sulfhydryl Oxidase by Molecular Engineering of the Shuttle Disulfide.
Authors: Vitu, E. / Bentzur, M. / Lisowsky, T. / Kaiser, C.A. / Fass, D.
History
DepositionJun 30, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 22, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Sulfhydryl oxidase Erv1p
B: Sulfhydryl oxidase Erv1p
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,53316
Polymers28,8092
Non-polymers2,72414
Water2,108117
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7140 Å2
ΔGint-178 kcal/mol
Surface area10840 Å2
MethodPISA
2
A: Sulfhydryl oxidase Erv1p
hetero molecules

A: Sulfhydryl oxidase Erv1p
hetero molecules

B: Sulfhydryl oxidase Erv1p
hetero molecules

B: Sulfhydryl oxidase Erv1p
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,06532
Polymers57,6184
Non-polymers5,44828
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_445-y-1,-x-1,-z+1/61
crystal symmetry operation5_555y,-x+y,z+1/61
crystal symmetry operation8_445x-y-1,-y-1,-z1
Buried area15220 Å2
ΔGint-378 kcal/mol
Surface area20740 Å2
MethodPISA
3
A: Sulfhydryl oxidase Erv1p
B: Sulfhydryl oxidase Erv1p
hetero molecules

A: Sulfhydryl oxidase Erv1p
B: Sulfhydryl oxidase Erv1p
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,06532
Polymers57,6184
Non-polymers5,44828
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_445-y-1,-x-1,-z+1/61
Buried area15340 Å2
ΔGint-371 kcal/mol
Surface area20610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.840, 82.840, 160.813
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522
DetailsThe biological assembly is the dimer of chains A and B.

-
Components

#1: Protein Sulfhydryl oxidase Erv1p


Mass: 14404.414 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Plasmid: pet15 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 plys S / References: UniProt: Q8LC15, UniProt: Q8GXX0*PLUS
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 117 / 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: 2.76 Å3/Da / Density % sol: 55.48 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 2.4
Details: 17% PEG 4000, 0.1M sodium acetate,0.5M ammonium sulfate, pH 2.4, VAPOR DIFFUSION, HANGING DROP, temperature 293K

-
Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11201
21001
Diffraction source
SourceSiteBeamlineTypeIDWavelength (Å)
ROTATING ANODERIGAKU11.5418
SYNCHROTRONESRF BM1420.979344, 0.979576, 0.911644
Detector
TypeIDDetectorDate
RIGAKU RAXIS IV1IMAGE PLATEJan 1, 2005
MARMOSAIC 225 mm CCD2CCDSep 14, 2005
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2MADMx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
11.54181
20.9793441
30.9795761
40.9116441
ReflectionResolution: 2.5→50 Å / Num. all: 11915 / Num. obs: 11820 / % possible obs: 99.2 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 11.1 % / Rsym value: 0.068 / Net I/σ(I): 14.2
Reflection shellResolution: 2.5→2.59 Å / Rsym value: 0.505 / % possible all: 100

-
Processing

Software
NameClassification
SHARPphasing
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MAD / Resolution: 2.5→50 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.267 844 random
Rwork0.228 --
all-11915 -
obs-11820 -
Refinement stepCycle: LAST / Resolution: 2.5→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1646 0 166 117 1929
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONo_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.2

+
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