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- PDB-5xto: Crystal structure of baculoviral sulfhydryl oxidase P33 (H114A mutant) -

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Basic information

Entry
Database: PDB / ID: 5xto
TitleCrystal structure of baculoviral sulfhydryl oxidase P33 (H114A mutant)
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 nucleopolyhedrovirus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.56 Å
AuthorsKuang, W. / Hu, Z. / Gong, P.
Funding support China, 1items
OrganizationGrant numberCountry
National Science Foundation of ChinaNo. 31570153 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
DepositionJun 20, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 13, 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 1.3Dec 25, 2019Group: Data collection / Category: reflns / reflns_shell
Item: _reflns.pdbx_Rpim_I_all / _reflns.pdbx_Rrim_I_all ..._reflns.pdbx_Rpim_I_all / _reflns.pdbx_Rrim_I_all / _reflns_shell.pdbx_Rpim_I_all / _reflns_shell.pdbx_Rrim_I_all
Revision 1.4Nov 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
Revision 1.5Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)140,9828
Polymers137,8394
Non-polymers3,1424
Water1,26170
1
A: FAD-linked sulfhydryl oxidase
B: FAD-linked sulfhydryl oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,4914
Polymers68,9202
Non-polymers1,5712
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5600 Å2
ΔGint-22 kcal/mol
Surface area22110 Å2
MethodPISA
2
C: FAD-linked sulfhydryl oxidase
D: FAD-linked sulfhydryl oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,4914
Polymers68,9202
Non-polymers1,5712
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5620 Å2
ΔGint-19 kcal/mol
Surface area22810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.132, 152.642, 75.885
Angle α, β, γ (deg.)90.000, 110.920, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
FAD-linked sulfhydryl oxidase / p33


Mass: 34459.871 Da / Num. of mol.: 4 / Mutation: H114A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Autographa californica nucleopolyhedrovirus
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.: 4 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 70 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.32 Å3/Da / Density % sol: 47 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.2 / Details: PEG3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.9793 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 3, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.555→60 Å / Num. obs: 37851 / % possible obs: 93.2 % / Redundancy: 3.8 % / Biso Wilson estimate: 41.16 Å2 / Rmerge(I) obs: 0.079 / Χ2: 0.98 / Net I/σ(I): 6.4 / Num. measured all: 142090
Reflection shellResolution: 2.56→2.65 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.484 / Num. unique all: 4044 / CC1/2: 0.999 / Χ2: 0.992 / % possible all: 91.9

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
HKL-2000V0.97.644data scaling
HKL-2000V0.97.644data reduction
PHENIX1.11.1_2575phasing
PDB_EXTRACT3.22data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3QZY

3qzy


Resolution: 2.56→37.55 Å / SU ML: 0.32 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 33.4
RfactorNum. reflection% reflection
Rfree0.246 1778 4.72 %
Rwork0.209 35912 -
obs0.21 37690 92.7 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 82.91 Å2 / Biso mean: 39.56 Å2 / Biso min: 17.12 Å2
Refinement stepCycle: final / Resolution: 2.56→37.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7948 0 212 70 8230
Biso mean--37.5 40.3 -
Num. residues----988
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 13

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.555-2.62410.33441610.26382627278889
2.6241-2.70130.30341320.25752736286892
2.7013-2.78840.3311250.24642716284191
2.7884-2.88810.27541250.24372713283891
2.8881-3.00360.32811270.24272731285892
3.0036-3.14030.30321310.2342702283391
3.1403-3.30580.23961240.22472720284491
3.3058-3.51270.24471230.21272713283691
3.5127-3.78370.24631170.19722760287792
3.7837-4.1640.24651730.19112739291293
4.164-4.76560.19211550.17062893304897
4.7656-6.00010.20511550.20172926308198
6.0001-37.55360.2311300.19652936306697

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