[English] 日本語
Yorodumi
- PDB-8gkp: Crystal Structure Analysis of Aspergillus fumigatus alkaline protease -

+
Open data


ID or keywords:

Loading...

-
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 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
Components

-
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

-
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 / Comment: protease inhibitor*YM
#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

-
Details

Has ligand of interestY
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
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 %

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more