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

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Basic information

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


oryzin / symbiont-mediated suppression of host complement activation / elastin catabolic process / fibrinogen binding / IgE binding / serine-type peptidase activity / protein catabolic process / peptidase activity / serine-type endopeptidase activity / proteolysis ...oryzin / symbiont-mediated suppression of host complement activation / elastin catabolic process / fibrinogen binding / IgE binding / serine-type peptidase activity / protein catabolic process / 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. / Peptidase S8, subtilisin, Ser-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 / Serine proteases, subtilase domain profile. / Peptidase S8, subtilisin-related / Peptidase S8/S53 domain superfamily / Subtilase family / Peptidase S8/S53 domain
Similarity search - Domain/homology
FORMIC ACID / DI(HYDROXYETHYL)ETHER / Alkaline protease 1
Similarity search - Component
Biological speciesAspergillus fumigatus Af293 (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.65 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)39,8447
Polymers39,5282
Non-polymers3165
Water2,918162
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3350 Å2
ΔGint-21 kcal/mol
Surface area14100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.255, 66.074, 86.794
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 / Proteasome endopeptidase complex / ALP / Aspergillopeptidase B / Aspergillus proteinase B / Elastase / Elastinolytic serine proteinase / Oryzin


Mass: 10798.985 Da / Num. of mol.: 1 / Fragment: N-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 / Proteasome endopeptidase complex / 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) / Gene: alp1, alk1, alp, AFUA_4G11800 / Production host: Escherichia coli (E. coli) / References: UniProt: P28296, oryzin

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Non-polymers , 5 types, 167 molecules

#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-FMT / FORMIC ACID / Formic acid


Mass: 46.025 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CH2O2
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 162 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.15 Å3/Da / Density % sol: 39 % / Description: Plate
Crystal growTemperature: 289 K / Method: evaporation / Details: PEG 1000, PEG 3350, MPD, MOPS/HEPES

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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: 1.65→52.573 Å / Num. all: 40727 / Num. obs: 40727 / % possible obs: 98.1 % / Redundancy: 3 % / Rpim(I) all: 0.052 / Rrim(I) all: 0.093 / Rsym value: 0.077 / Net I/av σ(I): 6.9 / Net I/σ(I): 6.8 / Num. measured all: 122123
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
1.65-1.7431.0680.71793559850.7411.3071.068199.7
1.74-1.8430.6951.11676556270.4820.8510.6951.599.6
1.84-1.972.80.391.11487452240.2720.4790.392.697.6
1.97-2.1330.2242.61494449240.1520.2720.2244.498.6
2.13-2.333.10.1415.11410745850.0940.170.1416.699.5
2.33-2.6130.10671239140840.070.1280.1068.498.4
2.61-3.012.90.07110.11025534990.0460.0850.07111.194.4
3.01-3.693.10.04913.3971231070.0320.0590.04916.698.5
3.69-5.2230.03815.9705823740.0250.0460.03820.196.1
5.22-36.2733.10.03117.9408213180.020.0370.03120.491.8

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
XDSdata reduction
SCALA3.3.22data scaling
PHASERphasing
REFMAC5.8.0135refinement
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.65→30.57 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.938 / WRfactor Rfree: 0.2404 / WRfactor Rwork: 0.1996 / FOM work R set: 0.6852 / SU B: 4.533 / SU ML: 0.133 / SU R Cruickshank DPI: 0.1167 / SU Rfree: 0.116 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.117 / ESU R Free: 0.116 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2468 2028 5 %RANDOM
Rwork0.2067 ---
obs0.2086 38658 97.57 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 85.7 Å2 / Biso mean: 29.376 Å2 / Biso min: 15.49 Å2
Baniso -1Baniso -2Baniso -3
1--2.17 Å2-0 Å20 Å2
2--2.89 Å2-0 Å2
3----0.71 Å2
Refinement stepCycle: final / Resolution: 1.65→30.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2777 0 19 162 2958
Biso mean--42.6 36.25 -
Num. residues----375
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0192867
X-RAY DIFFRACTIONr_angle_refined_deg1.4671.9353893
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9285378
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.55324.914116
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.18115438
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.8571510
X-RAY DIFFRACTIONr_chiral_restr0.1010.2444
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0212172
LS refinement shellResolution: 1.65→1.693 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.373 160 -
Rwork0.374 2846 -
all-3006 -
obs--99.54 %

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