[English] 日本語
Yorodumi
- PDB-5xki: Crystal structure of baculoviral sulfhydryl oxidase AcP33 (wide type) -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5xki
TitleCrystal structure of baculoviral sulfhydryl oxidase AcP33 (wide type)
ComponentsFAD-linked sulfhydryl oxidase
KeywordsOXIDOREDUCTASE / sulfhydryl oxidase
Function / homologyFAD-linked sulfhydryl oxidase / Baculovirus P33 / thiol oxidase / thiol oxidase activity / host cell cytoplasm / host cell nucleus / FLAVIN-ADENINE DINUCLEOTIDE / FAD-linked sulfhydryl oxidase
Function and homology information
Biological speciesAutographa californica nuclear polyhedrosis virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.46 Å
AuthorsKuang, W. / Hu, Z. / Gong, P.
Funding support China, 1items
OrganizationGrant numberCountry
National Science Foundation of China31570153 China
CitationJournal: J. Virol. / Year: 2017
Title: Three Conserved Regions in Baculovirus Sulfhydryl Oxidase P33 Are Critical for Enzymatic Activity and Function
Authors: Kuang, W. / Zhang, H. / Wang, M. / Zhou, N.Y. / Deng, F. / Wang, H. / Gong, P. / Hu, Z.
History
DepositionMay 7, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 20, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2017Group: Database references / Category: citation
Item: _citation.journal_abbrev / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed
Revision 1.2Dec 6, 2017Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.title
Revision 1.3Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: FAD-linked sulfhydryl oxidase
B: FAD-linked sulfhydryl oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,6254
Polymers69,0542
Non-polymers1,5712
Water66737
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6380 Å2
ΔGint-28 kcal/mol
Surface area22230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)145.742, 70.971, 73.396
Angle α, β, γ (deg.)90.000, 108.820, 90.000
Int Tables number5
Space group name H-MC121

-
Components

#1: Protein FAD-linked sulfhydryl oxidase / p33


Mass: 34526.941 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Autographa californica nuclear polyhedrosis virus
Gene: P33, ORF92 / Plasmid: pET28 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P41480, thiol oxidase
#2: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


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


Mass: 18.015 Da / Num. of mol.: 37 / 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: 2.6 Å3/Da / Density % sol: 52.72 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: glycerol ethoxylate

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 28, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.46→38.59 Å / Num. obs: 25814 / % possible obs: 99.6 % / Redundancy: 3.69 % / Biso Wilson estimate: 60.63 Å2 / Rmerge(I) obs: 0.075 / Rrim(I) all: 0.087 / Χ2: 1.13 / Net I/σ(I): 8.2 / Num. measured all: 95874 / Scaling rejects: 720
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. measured obsNum. unique allNum. unique obsRrim(I) allΧ2Rejects% possible all
2.46-2.553.740.4941.9963625921256325700.5761.415699.7
2.55-2.653.720.4192.3954625450.491.387399.8
2.65-2.773.730.3312.9970725910.3861.344599.9
2.77-2.923.720.263.7966925860.3041.295899.9
2.92-3.13.710.1824.8959725640.2131.138299.7
3.1-3.343.690.1187.3960025750.1381.059099.6
3.34-3.673.690.07910.7967925930.0930.9610399.8
3.67-4.213.680.06613.5952925740.0780.896599.8
4.21-5.33.640.06514.4953925980.0760.957199.7
5.3-38.593.540.04121.3937226250.0480.917798

-
Processing

Software
NameVersionClassification
PHENIX1.11.1_2575: ???refinement
d*TREK9.9.9.4Ddata scaling
d*TREK9.9.9.4Ddata reduction
PDB_EXTRACT3.22data extraction
PHENIX1.11.1_2575phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3QZY

3qzy


Resolution: 2.46→38.592 Å / SU ML: 0.35 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 31.77 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2643 1316 5.1 %
Rwork0.2087 24477 -
obs0.2115 25793 99.5 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 118.53 Å2 / Biso mean: 70.6381 Å2 / Biso min: 39.75 Å2
Refinement stepCycle: final / Resolution: 2.46→38.592 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4148 0 106 37 4291
Biso mean--68.41 63.24 -
Num. residues----512
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0084370
X-RAY DIFFRACTIONf_angle_d1.0125948
X-RAY DIFFRACTIONf_chiral_restr0.05657
X-RAY DIFFRACTIONf_plane_restr0.006721
X-RAY DIFFRACTIONf_dihedral_angle_d6.9872530
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 9

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.4601-2.55860.35721390.316627062845100
2.5586-2.6750.34051500.294226792829100
2.675-2.8160.32441550.294727182873100
2.816-2.99240.33381610.265826972858100
2.9924-3.22330.30761270.24922737286499
3.2233-3.54750.30791370.22227462883100
3.5475-4.06030.23451430.193127142857100
4.0603-5.11370.26161550.17727342889100
5.1137-38.59630.20741490.18042746289598

+
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