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- PDB-5xtr: Crystal structure of baculoviral sulfhydryl oxidase P33 (R127A, E... -

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Basic information

Entry
Database: PDB / ID: 5xtr
TitleCrystal structure of baculoviral sulfhydryl oxidase P33 (R127A, E183A 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 nuclear polyhedrosis virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 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 1.3Nov 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
Revision 1.4Oct 16, 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)140,6738
Polymers137,5314
Non-polymers3,1424
Water4,432246
1
A: FAD-linked sulfhydryl oxidase
C: FAD-linked sulfhydryl oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,3374
Polymers68,7662
Non-polymers1,5712
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5210 Å2
ΔGint-24 kcal/mol
Surface area22250 Å2
MethodPISA
2
B: FAD-linked sulfhydryl oxidase
D: FAD-linked sulfhydryl oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,3374
Polymers68,7662
Non-polymers1,5712
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5400 Å2
ΔGint-25 kcal/mol
Surface area22580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.136, 76.204, 80.231
Angle α, β, γ (deg.)84.320, 70.830, 69.270
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
FAD-linked sulfhydryl oxidase / p33


Mass: 34382.789 Da / Num. of mol.: 4 / Mutation: R127A, E183A
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.: 4 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 246 / 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: 47.03 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.3 / Details: PEG3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.9789 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 18, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9789 Å / Relative weight: 1
ReflectionResolution: 2.25→37.91 Å / Num. obs: 53132 / % possible obs: 90.5 % / Redundancy: 1.83 % / Biso Wilson estimate: 37.97 Å2 / Rmerge(I) obs: 0.057 / Rrim(I) all: 0.081 / Χ2: 1.22 / Net I/σ(I): 7.4
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsRrim(I) allΧ2% possible all
2.25-2.331.840.2442.254820.3441.2392.9
2.33-2.421.830.2042.60.2881.1693.4
2.42-2.531.830.1673.30.2371.2293.2
2.53-2.671.830.1244.30.1751.1392.8
2.67-2.831.830.0965.30.1361.0893.1
2.83-3.051.840.0836.20.1171.0192.1
3.05-3.361.820.068.80.0851.0988.9
3.36-3.851.790.04911.50.0691.285.1
3.85-4.841.80.04315.20.0611.4984.5
4.84-37.911.830.0416.90.0561.6588.6

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Processing

Software
NameVersionClassification
d*TREK9.9.9.4Ddata scaling
PHENIX1.11.1_2575phasing
PDB_EXTRACT3.22data extraction
PHENIX1.11.1_2575refinement
d*TREK9.9.9.4Ddata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3QZY

3qzy


Resolution: 2.25→37.883 Å / SU ML: 0.32 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 33.33
RfactorNum. reflection% reflection
Rfree0.2868 2388 4.5 %
Rwork0.2434 --
obs0.2454 53095 90.4 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 87.96 Å2 / Biso mean: 41.3415 Å2 / Biso min: 20.49 Å2
Refinement stepCycle: final / Resolution: 2.25→37.883 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7805 0 212 246 8263
Biso mean--39.44 43.89 -
Num. residues----976
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0088222
X-RAY DIFFRACTIONf_angle_d0.99611195
X-RAY DIFFRACTIONf_chiral_restr0.0491266
X-RAY DIFFRACTIONf_plane_restr0.0051341
X-RAY DIFFRACTIONf_dihedral_angle_d5.9324712
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 17

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.25-2.29590.3081320.27813110324292
2.2959-2.34580.3311150.28573059317493
2.3458-2.40040.35461480.29323074322293
2.4004-2.46040.39061530.30053108326193
2.4604-2.52690.37171350.28983063319893
2.5269-2.60130.34411590.28153067322693
2.6013-2.68520.32221410.27943066320793
2.6852-2.78110.31041390.26943078321793
2.7811-2.89250.36031560.27593016317292
2.8925-3.02410.31671330.27643043317692
3.0241-3.18340.35441030.26473008311190
3.1834-3.38270.31281210.24522909303088
3.3827-3.64370.29551440.22312809295385
3.6437-4.01010.23481430.20582762290584
4.0101-4.58950.22961070.20412825293285
4.5895-5.77890.24011520.21962760291284
5.7789-37.88810.26072070.23632950315791

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