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

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3qzy
TitleStructure of Baculovirus Sulfhydryl Oxidase Ac92
ComponentsBaculovirus sulfhydryl oxidase Ac92
KeywordsOXIDOREDUCTASE / flavin adenine dinucleotide / viral protein / 4-helix bundle / 5-helix bundle / sulfhydryl oxidase / nucleus
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
FLAVIN-ADENINE DINUCLEOTIDE / IMIDAZOLE / PHOSPHATE ION / FAD-linked sulfhydryl oxidase
Similarity search - Component
Biological speciesAutographa californica nucleopolyhedrovirus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.14 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
DepositionMar 7, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 15, 2012Provider: repository / Type: Initial release
Revision 1.1Sep 13, 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: Baculovirus sulfhydryl oxidase Ac92
B: Baculovirus sulfhydryl oxidase Ac92
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,8567
Polymers62,0262
Non-polymers1,8305
Water2,486138
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5440 Å2
ΔGint-30 kcal/mol
Surface area23020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.730, 50.730, 65.170
Angle α, β, γ (deg.)83.95, 79.01, 65.58
Int Tables number1
Space group name H-MP1

-
Components

#1: Protein Baculovirus sulfhydryl oxidase Ac92 / p33


Mass: 31013.012 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Autographa californica nucleopolyhedrovirus
Gene: Ac92, P33 / Plasmid: pET28 / 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.: 2 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#4: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 138 / 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: 2.42 Å3/Da / Density % sol: 49.09 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 9
Details: 4% PEG 2000 MME, 7% DMSO, 0.1M bicine, 0.05M arginine-HCl, 0.001M ZnCl2, pH 9, VAPOR DIFFUSION, HANGING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.97692 Å
DetectorType: ADSC Q315R / Detector: CCD / Date: Jun 22, 2010
RadiationMonochromator: Synchrotron / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97692 Å / Relative weight: 1
ReflectionResolution: 2.14→40.34 Å / Num. all: 31279 / Num. obs: 31279 / % possible obs: 97.6 % / Redundancy: 3.8 % / Rsym value: 0.075 / Net I/σ(I): 8.5
Reflection shellResolution: 2.14→2.26 Å / Redundancy: 3.8 % / Mean I/σ(I) obs: 3.1 / Num. unique all: 4477 / Rsym value: 0.399 / % possible all: 95.7

-
Processing

Software
NameVersionClassification
DNAdata collection
PHASERphasing
CNS1.2refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3P0K

3p0k


Resolution: 2.14→40.34 Å / σ(F): 2 / Stereochemistry target values: CNS
RfactorNum. reflectionSelection details
Rfree0.2698 2183 RANDOM
Rwork0.2305 --
all-32036 -
obs-31277 -
Refinement stepCycle: LAST / Resolution: 2.14→40.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4097 0 121 138 4356
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.00739
X-RAY DIFFRACTIONc_angle_deg1.04432
LS refinement shellResolution: 2.14→2.16 Å / Rfactor Rfree: 0.3183 / Rfactor Rwork: 0.2698

+
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