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

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Basic information

Entry
Database: PDB / ID: 8gko
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
FORMYL GROUP / IMIDAZOLE / Alkaline protease 1
Similarity search - Component
Biological speciesAspergillus fumigatus Af293 (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / AB INITIO PHASING / molecular replacement / Resolution: 1.06 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Alkaline protease 1
C: Alkaline protease 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,95811
Polymers39,5282
Non-polymers4309
Water8,701483
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3450 Å2
ΔGint-23 kcal/mol
Surface area14740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.605, 70.765, 78.555
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Alkaline protease ... , 2 types, 2 molecules AC

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


Mass: 10798.985 Da / Num. of mol.: 1 / Fragment: C-terminal residues 27-121
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aspergillus fumigatus Af293 (mold) / Strain: ATCC MYA-4609 / Af293 / CBS 101355 / FGSC A1100 / 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.: 1 / Fragment: C-terminal residues 122-403
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aspergillus fumigatus Af293 (mold) / Strain: ATCC MYA-4609 / Af293 / CBS 101355 / FGSC A1100 / Gene: alp1, alk1, alp, AFUA_4G11800 / Production host: Escherichia coli (E. coli) / References: UniProt: P28296, oryzin

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Non-polymers , 5 types, 492 molecules

#3: Chemical ChemComp-IMD / IMIDAZOLE


Mass: 69.085 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H5N2
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-FOR / FORMYL GROUP


Mass: 30.026 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: CH2O
#6: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 483 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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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 Å3/Da / Density % sol: 42.27 % / Description: Rod
Crystal growTemperature: 289 K / Method: evaporation
Details: polyethyleneglycol 550 monomethylether, polyethyleneglycol 20,000, MES/Imidazole buffer

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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: 1.06→52.577 Å / Num. all: 142896 / Num. obs: 142896 / % possible obs: 93.5 % / Redundancy: 3.8 % / Rpim(I) all: 0.043 / Rrim(I) all: 0.088 / Rsym value: 0.076 / Net I/av σ(I): 6.4 / Net I/σ(I): 8.6 / Num. measured all: 549701
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique obsRpim(I) allRrim(I) allRsym valueNet I/σ(I) obs% possible all
1.06-1.1221.1250.728789142740.9031.451.1250.765.2
1.12-1.192.90.7930.954757190400.5310.9610.7931.591.2
1.19-1.2740.6511.179459196340.3680.750.6512.599.4
1.27-1.374.10.4461.674785183150.2510.5130.4463.499.8
1.37-1.54.20.2682.771809169530.1480.3070.2685.399.8
1.5-1.684.40.1484.867294153860.080.1680.1488.699.8
1.68-1.944.30.0848.258437135600.0460.0970.08413.499.7
1.94-2.374.60.05212.552939115840.0270.0590.05221.999.8
2.37-3.354.40.0413.53930490060.0210.0460.0427.499.5
3.35-35.3824.30.03316.42212851440.0180.0380.03333.699.1

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
XDSdata reduction
SCALA3.3.22data scaling
Arcimboldophasing
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: AB INITIO PHASING / Resolution: 1.06→30.58 Å / Cor.coef. Fo:Fc: 0.981 / Cor.coef. Fo:Fc free: 0.976 / WRfactor Rfree: 0.1476 / WRfactor Rwork: 0.1276 / FOM work R set: 0.8397 / SU B: 1.096 / SU ML: 0.022 / SU R Cruickshank DPI: 0.0281 / SU Rfree: 0.0281 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.028 / ESU R Free: 0.028 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.16 7013 4.9 %RANDOM
Rwork0.1402 ---
obs0.1412 135789 93.24 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 71.18 Å2 / Biso mean: 13.191 Å2 / Biso min: 5.7 Å2
Baniso -1Baniso -2Baniso -3
1--0.02 Å2-0 Å2-0 Å2
2---0.07 Å20 Å2
3---0.09 Å2
Refinement stepCycle: final / Resolution: 1.06→30.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2787 0 59 483 3329
Biso mean--34.13 26.38 -
Num. residues----377
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0193027
X-RAY DIFFRACTIONr_bond_other_d0.0020.022815
X-RAY DIFFRACTIONr_angle_refined_deg1.3841.9384127
X-RAY DIFFRACTIONr_angle_other_deg1.03836494
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2345413
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.52424.959121
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.74815472
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.9191511
X-RAY DIFFRACTIONr_chiral_restr0.0930.2464
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.023614
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02697
X-RAY DIFFRACTIONr_rigid_bond_restr3.5535842
X-RAY DIFFRACTIONr_sphericity_free24.5765106
X-RAY DIFFRACTIONr_sphericity_bonded7.17556155
LS refinement shellResolution: 1.06→1.088 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.37 309 -
Rwork0.35 6095 -
all-6404 -
obs--56.95 %

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