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- PDB-8u45: Crystal Structure Analysis of Aspergillus fumigatus alkaline protease -

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Basic information

Entry
Database: PDB / ID: 8u45
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
DI(HYDROXYETHYL)ETHER / Alkaline protease 1
Similarity search - Component
Biological speciesAspergillus fumigatus Af293 (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 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
DepositionSep 8, 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)40,86610
Polymers40,1532
Non-polymers7128
Water2,126118
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3880 Å2
ΔGint-19 kcal/mol
Surface area14360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.910, 94.592, 52.925
Angle α, β, γ (deg.)90.00, 103.20, 90.00
Int Tables number4
Space group name H-MP1211

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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: 11424.656 Da / Num. of mol.: 1 / Fragment: Pro-domain of oryzin, residues 21-121
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 (E. coli) / 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: Oryzin catalytic domain, 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 , 4 types, 126 molecules

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


Mass: 106.120 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C4H10O3
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 118 / 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: 2.68 Å3/Da / Density % sol: 54.1 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: PEG 1000, PEG 3350, MPD; L-glutamate, DL-alanine, glycine, DL-lysine, and DL-serine; MOPS/HEPES, pH 7.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL14-1 / Wavelength: 1.77115 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 20, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.77115 Å / Relative weight: 1
ReflectionResolution: 2.1→38.21 Å / Num. obs: 22839 / % possible obs: 95.1 % / Redundancy: 4.6 % / CC1/2: 0.993 / Rmerge(I) obs: 0.111 / Rpim(I) all: 0.062 / Rrim(I) all: 0.136 / Net I/σ(I): 5.5 / Num. measured all: 105471
Reflection shellResolution: 2.1→2.21 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.874 / Num. unique obs: 2900 / CC1/2: 0.331 / Rpim(I) all: 0.537 / Rrim(I) all: 1

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
SCALAdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→30.53 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.941 / SU B: 7.35 / SU ML: 0.182 / Cross valid method: THROUGHOUT / ESU R: 0.226 / ESU R Free: 0.184 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.22958 1158 5.1 %RANDOM
Rwork0.19116 ---
obs0.19329 21626 94.73 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 38.513 Å2
Baniso -1Baniso -2Baniso -3
1--1.82 Å20 Å2-1.7 Å2
2--3.43 Å20 Å2
3----0.73 Å2
Refinement stepCycle: 1 / Resolution: 2.1→30.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2760 0 44 118 2922
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0192849
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.7671.9413857
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.215372
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.39225.133113
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.65315429
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.759158
X-RAY DIFFRACTIONr_chiral_restr0.1180.2439
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0212134
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.9873.631494
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it3.9915.4181864
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it4.0833.9741355
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined6.9731.1294387
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.1→2.154 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.315 69 -
Rwork0.348 1286 -
obs--75.91 %

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