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- PDB-5xtq: Crystal structure of baculoviral sulfhydryl oxidase P33 (H227D mutant) -

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Basic information

Entry
Database: PDB / ID: 5xtq
TitleCrystal structure of baculoviral sulfhydryl oxidase P33 (H227D 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: 2.04 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

Downloads & links

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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)141,52612
Polymers138,0164
Non-polymers3,5118
Water5,747319
1
A: FAD-linked sulfhydryl oxidase
C: FAD-linked sulfhydryl oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,7636
Polymers69,0082
Non-polymers1,7554
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6250 Å2
ΔGint-24 kcal/mol
Surface area22140 Å2
MethodPISA
2
B: FAD-linked sulfhydryl oxidase
D: FAD-linked sulfhydryl oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,7636
Polymers69,0082
Non-polymers1,7554
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6430 Å2
ΔGint-24 kcal/mol
Surface area23170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.098, 76.040, 80.631
Angle α, β, γ (deg.)84.610, 71.270, 69.000
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
FAD-linked sulfhydryl oxidase / p33


Mass: 34503.883 Da / Num. of mol.: 4 / Mutation: H227D
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: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 319 / 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: 46.99 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.4 / Details: PEG3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 26, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.04→50 Å / Num. obs: 75844 / % possible obs: 96.5 % / Redundancy: 1.9 % / Biso Wilson estimate: 26.4 Å2 / Rmerge(I) obs: 0.035 / Χ2: 0.818 / Net I/σ(I): 18.9 / Num. measured all: 143698
Reflection shellResolution: 2.04→2.11 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.102 / Num. unique all: 7381 / CC1/2: 0.995 / Χ2: 0.479 / % possible all: 95.8

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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: 2.04→27.57 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.99 / Phase error: 24.04
RfactorNum. reflection% reflection
Rfree0.223 3008 4.87 %
Rwork0.186 58709 -
obs0.188 61717 78.5 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 71.25 Å2 / Biso mean: 28.47 Å2 / Biso min: 11.5 Å2
Refinement stepCycle: final / Resolution: 2.04→27.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8083 0 236 319 8638
Biso mean--28.01 31.74 -
Num. residues----999
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 21

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.0434-2.07690.28431350.19232551268672
2.0769-2.11270.30061260.19992719284575
2.1127-2.15110.24281370.17712662279975
2.1511-2.19240.24581430.17832662280575
2.1924-2.23720.23131150.17862710282575
2.2372-2.28580.25071340.172674280876
2.2858-2.33890.25921330.17832706283976
2.3389-2.39740.22521510.17522756290777
2.3974-2.46220.25581420.18592786292878
2.4622-2.53460.25891360.18792782291878
2.5346-2.61630.24771120.18312805291779
2.6163-2.70970.2423980.192861295978
2.7097-2.81810.21861250.20412853297880
2.8181-2.94630.2551340.21162869300380
2.9463-3.10140.2581500.20962877302781
3.1014-3.29540.24711910.19892845303681
3.2954-3.54940.21681320.18212944307683
3.5494-3.90570.22841800.17312890307082
3.9057-4.46870.20132180.16562867308582
4.4687-5.62230.16811710.17252838300981
5.6223-27.57030.19251450.20273052319785

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