[English] 日本語
Yorodumi
- PDB-4e0h: Crystal structure of FAD binding domain of Erv1 from Saccharomyce... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4e0h
TitleCrystal structure of FAD binding domain of Erv1 from Saccharomyces cerevisiae
ComponentsMitochondrial FAD-linked sulfhydryl oxidase ERV1
KeywordsOXIDOREDUCTASE / four-helix bundle / Flavin-linked sulfhydryl oxidase / FAD binding / oxidation / mitochondrial intermembrane space
Function / homology
Function and homology information


flavin-dependent sulfhydryl oxidase activity / thiol oxidase / thiol oxidase activity / protein import into mitochondrial intermembrane space / mitochondrial intermembrane space / flavin adenine dinucleotide binding / cellular response to oxidative stress / intracellular iron ion homeostasis / mitochondrion
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 / Mitochondrial FAD-linked sulfhydryl oxidase ERV1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsGuo, P.C. / Ma, J.D. / Jiang, Y.L. / Wang, S.J. / Hu, T.T. / Chen, Y.X. / Zhou, C.Z.
CitationJournal: J.Biol.Chem. / Year: 2012
Title: Structure of yeast sulfhydryl oxidase erv1 reveals electron transfer of the disulfide relay system in the mitochondrial intermembrane space
Authors: Guo, P.C. / Ma, J.D. / Jiang, Y.L. / Wang, S.J. / Bao, Z.Z. / Yu, X.J. / Chen, Y. / Zhou, C.Z.
History
DepositionMar 4, 2012Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Aug 29, 2012Provider: repository / Type: Initial release
Revision 1.1Jan 30, 2013Group: Database references
Revision 1.2Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Mitochondrial FAD-linked sulfhydryl oxidase ERV1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,5842
Polymers12,7981
Non-polymers7861
Water37821
1
A: Mitochondrial FAD-linked sulfhydryl oxidase ERV1
hetero molecules

A: Mitochondrial FAD-linked sulfhydryl oxidase ERV1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,1684
Polymers25,5972
Non-polymers1,5712
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_545x,-y-1,-z1
Buried area4680 Å2
ΔGint-30 kcal/mol
Surface area12010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)38.553, 46.599, 58.880
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP22121

-
Components

#1: Protein Mitochondrial FAD-linked sulfhydryl oxidase ERV1 / 14 kDa regulatory protein / Essential for respiration and vegetative growth protein 1


Mass: 12798.471 Da / Num. of mol.: 1 / Fragment: FAD binding domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: s288c / Gene: ERV1 / Plasmid: pET28 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P27882, thiol oxidase
#2: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE / Flavin adenine dinucleotide


Mass: 785.550 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 21 / 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: 2.07 Å3/Da / Density % sol: 40.47 %
Crystal growTemperature: 300 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 25% polyethylene glycol 3350, 0.2M Ammonium acetate, 0.1M Tris-HCl, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 300K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.979 Å
DetectorDetector: CCD / Date: Jan 7, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. all: 7555 / Num. obs: 7532 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 10.4 % / Rmerge(I) obs: 0.064 / Net I/σ(I): 30.9
Reflection shellResolution: 2→2.07 Å / Redundancy: 10.5 % / Rmerge(I) obs: 0.238 / Mean I/σ(I) obs: 10.68 / Num. unique all: 727 / % possible all: 100

-
Processing

Software
NameVersionClassification
HKL-2000data collection
AMoREphasing
REFMAC5.5.0072refinement
HKL-2000data reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1OQC

1oqc


Resolution: 2→50 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.938 / SU B: 9.157 / SU ML: 0.116 / Cross valid method: THROUGHOUT / ESU R: 0.211 / ESU R Free: 0.171 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22874 346 4.6 %RANDOM
Rwork0.19228 ---
obs0.19399 7185 99.46 %-
all-7224 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 35.154 Å2
Baniso -1Baniso -2Baniso -3
1-3.15 Å20 Å20 Å2
2---2.18 Å20 Å2
3----0.97 Å2
Refinement stepCycle: LAST / Resolution: 2→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms890 0 53 21 964
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.021978
X-RAY DIFFRACTIONr_angle_refined_deg1.7531.9791330
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2185104
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.02924.11851
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.28415165
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.364156
X-RAY DIFFRACTIONr_chiral_restr0.1110.2123
X-RAY DIFFRACTIONr_gen_planes_refined0.010.021745
X-RAY DIFFRACTIONr_mcbond_it1.0741.5525
X-RAY DIFFRACTIONr_mcangle_it2.1412843
X-RAY DIFFRACTIONr_scbond_it3.4353453
X-RAY DIFFRACTIONr_scangle_it5.6874.5487
LS refinement shellResolution: 2.003→2.055 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.203 18 -
Rwork0.174 494 -
obs--96.42 %
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)
11.314-0.02810.2061.8726-0.65591.69350.0187-0.07170.006-0.06870.05320.1918-0.13780.1071-0.07180.0564-0.0138-0.01110.01910.00520.0323-10.8449-15.7921-6.9097
22.48350.11021.81243.7521-1.17274.75920.10190.1325-0.1208-0.20510.05810.1552-0.00950.1185-0.160.02370.0005-0.01290.0083-0.00450.0129-10.4929-17.8077-8.8194
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A84 - 188
2X-RAY DIFFRACTION1A201
3X-RAY DIFFRACTION2A301 - 321

+
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://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