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- PDB-8gkp: Crystal Structure Analysis of Aspergillus fumigatus alkaline protease -

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Basic information

Entry
Database: PDB / ID: 8gkp
TitleCrystal Structure Analysis of Aspergillus fumigatus alkaline protease
Components(Alkaline protease ...) x 2
KeywordsHYDROLASE / alpha-beta hydrolase
Function / homology
Function and homology information


oryzin / symbiont-mediated suppression of host immunoglobulin-mediated immune response / symbiont-mediated suppression of host complement activation / elastin catabolic process / fibrinogen binding / IgE binding / serine-type peptidase activity / peptidase activity / serine-type endopeptidase activity / proteolysis ...oryzin / symbiont-mediated suppression of host immunoglobulin-mediated immune response / symbiont-mediated suppression of host complement activation / elastin catabolic process / fibrinogen binding / IgE binding / serine-type peptidase activity / peptidase activity / serine-type endopeptidase activity / proteolysis / extracellular space / extracellular region
Similarity search - Function
Proteinase K-like catalytic domain / Peptidase S8 propeptide/proteinase inhibitor I9 / Peptidase inhibitor I9 / Peptidase S8 propeptide/proteinase inhibitor I9 superfamily / Peptidase S8, subtilisin, His-active site / : / Serine proteases, subtilase family, histidine active site. / Serine proteases, subtilase family, aspartic acid active site. / Peptidase S8, subtilisin, Asp-active site / Serine proteases, subtilase family, serine active site. ...Proteinase K-like catalytic domain / Peptidase S8 propeptide/proteinase inhibitor I9 / Peptidase inhibitor I9 / Peptidase S8 propeptide/proteinase inhibitor I9 superfamily / Peptidase S8, subtilisin, His-active site / : / Serine proteases, subtilase family, histidine active site. / Serine proteases, subtilase family, aspartic acid active site. / Peptidase S8, subtilisin, Asp-active site / Serine proteases, subtilase family, serine active site. / Peptidase S8, subtilisin, Ser-active site / Peptidase S8, subtilisin-related / Serine proteases, subtilase domain profile. / Peptidase S8/S53 domain superfamily / Subtilase family / Peptidase S8/S53 domain
Similarity search - Domain/homology
FORMIC ACID / DI(HYDROXYETHYL)ETHER / PHENYLMETHYLSULFONYL FLUORIDE / Alkaline protease 1
Similarity search - Component
Biological speciesAspergillus fumigatus Af293 (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 Å
AuthorsFernandez, D. / Diec, D.D.L. / Guo, W. / Russi, S.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Sci Rep / Year: 2023
Title: Targeting Aspergillus allergen oryzin with a chemical probe at atomic precision.
Authors: Pattelli, O.N. / Diec, D.D.L. / Guo, W. / Russi, S. / Fernandez, D.
History
DepositionMar 20, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 1, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
I: Alkaline protease 1
C: Alkaline protease 1
J: Alkaline protease 1
D: Alkaline protease 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,18122
Polymers79,0554
Non-polymers1,12618
Water7,458414
1
I: Alkaline protease 1
C: Alkaline protease 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,22214
Polymers39,5282
Non-polymers69412
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4610 Å2
ΔGint-39 kcal/mol
Surface area14210 Å2
MethodPISA
2
J: Alkaline protease 1
D: Alkaline protease 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,9598
Polymers39,5282
Non-polymers4316
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3570 Å2
ΔGint-19 kcal/mol
Surface area13930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.092, 75.218, 87.929
Angle α, β, γ (deg.)90.000, 101.390, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Alkaline protease ... , 2 types, 4 molecules IJCD

#1: Protein Alkaline protease 1 / ALP / Aspergillopeptidase B / Aspergillus proteinase B / Elastase / Elastinolytic serine proteinase / Oryzin


Mass: 10798.985 Da / Num. of mol.: 2 / Fragment: C-terminal residues 27-121
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aspergillus fumigatus Af293 (mold) / Gene: alp1, alk1, alp, AFUA_4G11800 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P28296, oryzin
#2: Protein Alkaline protease 1 / ALP / Aspergillopeptidase B / Aspergillus proteinase B / Elastase / Elastinolytic serine proteinase / Oryzin


Mass: 28728.674 Da / Num. of mol.: 2 / Fragment: C-terminal residues 122-403
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aspergillus fumigatus Af293 (mold) / Gene: alp1, alk1, alp, AFUA_4G11800 / Production host: Escherichia coli (E. coli) / References: UniProt: P28296, oryzin

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Non-polymers , 6 types, 432 molecules

#3: Chemical
ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: CH2O2
#4: Chemical ChemComp-PMF / PHENYLMETHYLSULFONYL FLUORIDE / PMSF


Mass: 174.193 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H7FO2S / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Na
#6: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#7: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 414 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
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: 1.96 Å3/Da / Density % sol: 41.29 % / Description: Plate
Crystal growTemperature: 289 K / Method: evaporation
Details: polyethyleneglycol 550 monomethylether, polyethyleneglycol 20,000, MES/Imidazole

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.97946 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 17, 2021
Details: Flat Si Rh coated M0, Kirkpatrick-Baez flat bent Si M1 & M2
RadiationMonochromator: Liquid nitrogen-cooled double crystal, non fixed exit slit
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 1.55→86.197 Å / Num. all: 91847 / Num. obs: 91847 / % possible obs: 97.3 % / Redundancy: 3.9 % / Rpim(I) all: 0.037 / Rrim(I) all: 0.074 / Rsym value: 0.064 / Net I/av σ(I): 9.3 / Net I/σ(I): 10.9 / Num. measured all: 355823
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsRpim(I) allRrim(I) allRsym value% possible all
1.55-1.633.80.9450.8130920.5531.0990.94595.6
1.63-1.733.90.6231.2126370.3570.7210.62397.4
1.73-1.853.80.391.9119000.230.4550.3997.3
1.85-23.90.2083.7109460.1210.2420.20896.4
2-2.193.90.1226.2103290.0710.1420.12298.3
2.19-2.453.80.0789.792160.0460.0910.07896.9
2.45-2.8340.05213.983080.030.060.05299
2.83-3.473.80.03717.469240.0220.0440.03797.7
3.47-4.940.02722.454880.0150.0310.02799.2
4.9-37.6093.80.0262030070.0150.030.02697.3

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Processing

Software
NameVersionClassification
XDSdata reduction
SCALA3.3.22data scaling
REFMAC5.8.0135refinement
PDB_EXTRACT3.27data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.55→30.2 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.958 / SU B: 4.441 / SU ML: 0.068 / SU R Cruickshank DPI: 0.106 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.106 / ESU R Free: 0.087 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2065 4546 5 %RANDOM
Rwork0.1529 ---
obs0.1556 87267 97.08 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 93.97 Å2 / Biso mean: 24.11 Å2 / Biso min: 10.15 Å2
Baniso -1Baniso -2Baniso -3
1-0.5 Å20 Å2-0.09 Å2
2--0.08 Å20 Å2
3----0.5 Å2
Refinement stepCycle: final / Resolution: 1.55→30.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5542 0 68 414 6024
Biso mean--41.6 32.35 -
Num. residues----750
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0195802
X-RAY DIFFRACTIONr_angle_refined_deg1.5151.9397881
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1895768
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.77924.957232
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.7315882
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.0821519
X-RAY DIFFRACTIONr_chiral_restr0.1210.2896
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0214407
X-RAY DIFFRACTIONr_rigid_bond_restr3.30935802
X-RAY DIFFRACTIONr_sphericity_free22.5785145
X-RAY DIFFRACTIONr_sphericity_bonded11.66255967
LS refinement shellResolution: 1.55→1.59 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.326 317 -
Rwork0.275 6202 -
all-6519 -
obs--93.76 %

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