[English] 日本語
Yorodumi
- PDB-3p0k: Structure of Baculovirus Sulfhydryl Oxidase Ac92 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3p0k
TitleStructure of Baculovirus Sulfhydryl Oxidase Ac92
Componentssulfhydryl oxidase
KeywordsOxidoreductase / Viral protein / 4-helix bundle / 5-helix bundle / flavin adenine dinucleotide / sulfhydryl oxidase
Function / homology
Function and homology information


thiol oxidase / thiol oxidase activity / host cell cytoplasm / host cell nucleus
Similarity search - Function
FAD-linked sulfhydryl oxidase / Baculovirus P33
Similarity search - Domain/homology
ACETATE ION / FLAVIN-ADENINE DINUCLEOTIDE / IMIDAZOLE / FAD-linked sulfhydryl oxidase
Similarity search - Component
Biological speciesAutographa californica nucleopolyhedrovirus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.47 Å
AuthorsHakim, M. / Fass, D.
CitationJournal: J.Virol. / Year: 2011
Title: Structure of a baculovirus sulfhydryl oxidase, a highly divergent member of the erv flavoenzyme family.
Authors: Hakim, M. / Mandelbaum, A. / Fass, D.
History
DepositionSep 29, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 7, 2011Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: sulfhydryl oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,5974
Polymers31,6831
Non-polymers9143
Water3,513195
1
A: sulfhydryl oxidase
hetero molecules

A: sulfhydryl oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,1938
Polymers63,3662
Non-polymers1,8276
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area7360 Å2
ΔGint-22 kcal/mol
Surface area22830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.765, 80.839, 65.053
Angle α, β, γ (deg.)90.00, 105.95, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-299-

HOH

21A-329-

HOH

31A-385-

HOH

-
Components

#1: Protein sulfhydryl oxidase / 33 kDa early protein homolog / p33


Mass: 31682.828 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Autographa californica nucleopolyhedrovirus
Gene: Ac92, P33 / Plasmid: pET-28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P41480, thiol oxidase
#2: Chemical ChemComp-IMD / IMIDAZOLE


Mass: 69.085 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H5N2
#3: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#4: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 195 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 2.22 Å3/Da / Density % sol: 44.72 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.4
Details: 0.1 M acetic acid, 50 mM arginine-HCl, 750 mM NaCl, 5% ethanol, 24% PEG 5000-MME, pH 4.4, VAPOR DIFFUSION, HANGING DROP, temperature 293K

-
Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.97692 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 22, 2010
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2MADMx-ray1
Radiation wavelengthWavelength: 0.97692 Å / Relative weight: 1
ReflectionResolution: 1.47→50 Å / Num. obs: 46687 / % possible obs: 99.1 % / Observed criterion σ(I): -3 / Redundancy: 6.8 % / Rsym value: 0.069 / Net I/σ(I): 19.2
Reflection shellResolution: 1.47→1.5 Å / Redundancy: 5.7 % / Mean I/σ(I) obs: 2.54 / Num. unique all: 2322 / Rsym value: 1 / % possible all: 99.1

-
Processing

Software
NameVersionClassification
PHENIXmodel building
CNS1.1refinement
HKL-2000data reduction
SCALEPACKdata scaling
PHENIXphasing
RefinementMethod to determine structure: MAD / Resolution: 1.47→50 Å / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.2335 3259 RANDOM
Rwork0.208 --
obs-46375 -
Refinement stepCycle: LAST / Resolution: 1.47→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2160 0 62 195 2417
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.00538
X-RAY DIFFRACTIONc_angle_deg0.95014
LS refinement shellResolution: 1.47→1.48 Å
RfactorNum. reflection
Rfree0.3317 55
Rwork0.3316 -
obs-821

+
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